AMBER Archive (2009) - By Thread

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Starting: Thu Jan 01 2009 - 21:37:45 CST
Ending: Sat Nov 07 2009 - 15:08:20 CST

AMBER: energy jumps during molecule minimization Paul Ledbetter (Thu Jan 01 2009 - 21:33:30 CST)
- Re: AMBER: energy jumps during molecule minimization David A. Case (Fri Jan 02 2009 - 06:48:23 CST)
Re: AMBER: SMD-related questions Gustavo Seabra (Fri Jan 02 2009 - 07:21:53 CST)
Re: AMBER: RMS plot Carlos Simmerling (Fri Jan 02 2009 - 08:08:44 CST)
- RE: AMBER: RMS plot Duggan, Brendan M. (Tue Jan 06 2009 - 13:54:04 CST)
  - Re: AMBER: RMS plot Carlos Simmerling (Tue Jan 06 2009 - 13:57:50 CST)
Re: AMBER: a question about ff03ua oguz gurbulak (Fri Jan 02 2009 - 09:30:46 CST)
- Re: AMBER: a question about ff03ua David A. Case (Fri Jan 02 2009 - 10:35:15 CST)
- Re: AMBER: a question about ff03ua FyD (Fri Jan 02 2009 - 14:20:37 CST)
AMBER: apparent error in closest function in ptraj 10 Roman Osman (Fri Jan 02 2009 - 09:54:48 CST)
- Re: AMBER: apparent error in closest function in ptraj 10 D.J. Cole (Fri Jan 02 2009 - 10:06:01 CST)
  - Re: AMBER: apparent error in closest function in ptraj 10 Roman Osman (Fri Jan 02 2009 - 11:37:09 CST)
AMBER: Dielectric constant musa özboyacý (Sat Jan 03 2009 - 12:54:06 CST)
AMBER: IMPORTANT INFORMATION: Notice regarding transition of AMBER mailing list to new address. Ross Walker (Sat Jan 03 2009 - 16:12:19 CST)
AMBER: CHCl3 solvent box WJ Ding (Sun Jan 04 2009 - 16:24:48 CST)
- Re: AMBER: CHCl3 solvent box David A. Case (Mon Jan 05 2009 - 07:48:44 CST)
  - Re: AMBER: CHCl3 solvent box WJ Ding (Mon Jan 05 2009 - 15:21:32 CST)
AMBER: reg sander crashing on more than 32 cores over IB Amit Bajaj (Mon Jan 05 2009 - 00:33:15 CST)
- Re: AMBER: reg sander crashing on more than 32 cores over IB David A. Case (Mon Jan 05 2009 - 06:47:01 CST)
AMBER: bug of the mm_pbsa module in ambertools 1.2 Ye Mei (Mon Jan 05 2009 - 09:28:02 CST)
- Re: AMBER: bug of the mm_pbsa module in ambertools 1.2 Scott Brozell (Tue Jan 06 2009 - 12:59:15 CST)
AMBER: ligand parameter Bo Baker (Mon Jan 05 2009 - 16:05:18 CST)
- RE: AMBER: ligand parameter Ross Walker (Mon Jan 05 2009 - 23:48:13 CST)
  - [AMBER] Re: AMBER: ligand parameter Bo Baker (Tue Jan 06 2009 - 21:59:19 CST)
AMBER: error in amber 10 archana sonawani (Tue Jan 06 2009 - 01:19:03 CST)
- Re: AMBER: error in amber 10 David A. Case (Tue Jan 06 2009 - 06:18:23 CST)
  - Re: AMBER: error in amber 10 David A. Case (Tue Jan 06 2009 - 06:28:54 CST)
AMBER: questions about equilibram wei zhang (Tue Jan 06 2009 - 05:18:47 CST)
- [AMBER] Re: AMBER: questions about equilibram David A. Case (Wed Jan 07 2009 - 06:54:10 CST)
  - RE: [AMBER] Re: AMBER: questions about equilibram wei zhang (Tue Jan 13 2009 - 06:58:51 CST)
AMBER: Re: nmode error: bad nonbon (amber 10) Jeremy Harris (Tue Jan 06 2009 - 07:37:21 CST)
- Re: AMBER: Re: nmode error: bad nonbon (amber 10) David A. Case (Tue Jan 06 2009 - 08:32:48 CST)
  - [AMBER] Re: AMBER: Re: nmode error: bad nonbon (amber 10) Jeremy Harris (Tue Jan 13 2009 - 15:58:36 CST)
    - Re: [AMBER] Re: AMBER: Re: nmode error: bad nonbon (amber 10) David A. Case (Wed Jan 14 2009 - 07:13:18 CST)
AMBER: install amber10 wl2290_at_columbia.edu (Tue Jan 06 2009 - 11:23:01 CST)
- Re: AMBER: install amber10 Scott Brozell (Tue Jan 06 2009 - 13:33:21 CST)
AMBER: problem with ptraj image command in Amber 10? Ryan Pavlovicz (Tue Jan 06 2009 - 11:28:27 CST)
- Re: AMBER: problem with ptraj image command in Amber 10? Carlos Simmerling (Tue Jan 06 2009 - 11:37:51 CST)
AMBER: xleap problem Bala subramanian (Tue Jan 06 2009 - 12:57:53 CST)
- Re: AMBER: xleap problem Carlos Simmerling (Tue Jan 06 2009 - 13:05:31 CST)
  - Re: AMBER: xleap problem Bala subramanian (Tue Jan 06 2009 - 13:43:00 CST)
Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) Scott Brozell (Tue Jan 06 2009 - 13:23:29 CST)
AMBER: IMPORTANT Information regarding AMBER Mailing List - please read. Ross Walker (Tue Jan 06 2009 - 14:40:00 CST)
AMBER: mail list Mark M Huntress (Tue Jan 06 2009 - 17:06:57 CST)
- [AMBER] RE: AMBER: mail list Ross Walker (Tue Jan 06 2009 - 17:47:08 CST)
  - Re: [AMBER] RE: AMBER: mail list James W. Caldwell (Tue Jan 06 2009 - 19:24:12 CST)
  - Re: [AMBER] RE: AMBER: mail list M. L. Dodson (Wed Jan 07 2009 - 10:04:02 CST)
[AMBER] amber@ambermd.org open for business Ross Walker (Tue Jan 06 2009 - 17:34:31 CST)
AMBER: REMINDER: The amber@scripps.edu mailing list is now CLOSED Ross Walker (Tue Jan 06 2009 - 17:40:50 CST)
[AMBER] TEST Message - please ignore. Ross Walker (Tue Jan 06 2009 - 19:00:39 CST)
[AMBER] AMBER: Problems in solvation with xleap vallespardojl_at_chem.leidenuniv.nl (Wed Jan 07 2009 - 07:39:56 CST)
[AMBER] MD Beale, John (Wed Jan 07 2009 - 08:40:07 CST)
- RE: [AMBER] MD Ross Walker (Wed Jan 07 2009 - 18:33:46 CST)
[AMBER] four prepin/frcmod files be read simultaneously by leap Yi Mao (Wed Jan 07 2009 - 08:46:05 CST)
- Re: [AMBER] four prepin/frcmod files be read simultaneously by leap rpaduri_at_chem.wayne.edu (Wed Jan 07 2009 - 10:05:09 CST)
  - Re: [AMBER] four prepin/frcmod files be read simultaneously by leap Yi Mao (Wed Jan 07 2009 - 10:38:52 CST)
    - Re: [AMBER] four prepin/frcmod files be read simultaneously by leap David A. Case (Wed Jan 07 2009 - 12:39:56 CST)
[AMBER] PBSA: PB bomb in pb_setgrd() Larry Layne (Wed Jan 07 2009 - 09:33:57 CST)
- RE: [AMBER] PBSA: PB bomb in pb_setgrd() Ray Luo (Wed Jan 07 2009 - 12:24:15 CST)
[AMBER] RE: RE: amber force filed for RNA Ross Walker (Wed Jan 07 2009 - 10:49:41 CST)
[AMBER] RE: same result Ross Walker (Wed Jan 07 2009 - 10:59:39 CST)
- Re: [AMBER] RE: same result zgong.hust (Thu Jan 08 2009 - 02:49:29 CST)
[AMBER] Amber Parameters for Iron Heme covalently boud to carbon monoxide Osmar Norberto de Souza (Wed Jan 07 2009 - 12:23:06 CST)
[AMBER] PHOSPHOTHREONINE Khaled Barakat (Wed Jan 07 2009 - 13:11:43 CST)
- Re: [AMBER] PHOSPHOTHREONINE David A. Case (Wed Jan 07 2009 - 13:29:35 CST)
[AMBER] Using GAFF with a covalently bound ligand or label Sale, Kenneth L (Wed Jan 07 2009 - 19:30:10 CST)
- Re: [AMBER] Using GAFF with a covalently bound ligand or label David A. Case (Wed Jan 07 2009 - 20:42:27 CST)
- Re: [AMBER] Using GAFF with a covalently bound ligand or label Markus Kaukonen (Fri Jan 16 2009 - 00:31:53 CST)
  - Re: [AMBER] Using GAFF with a covalently bound ligand or label FyD (Fri Jan 16 2009 - 03:13:43 CST)
[AMBER] Non-planarity of amide atoms after optimization Sanghwa Han (Wed Jan 07 2009 - 21:17:18 CST)
[AMBER] how many processors for parallel test michael (Thu Jan 08 2009 - 05:01:41 CST)
- Re: [AMBER] how many processors for parallel test David A. Case (Thu Jan 08 2009 - 06:08:06 CST)
  - Re: [AMBER] how many processors for parallel test michael bane (Thu Jan 08 2009 - 07:31:31 CST)
    - Re: [AMBER] how many processors for parallel test David A. Case (Thu Jan 08 2009 - 07:44:52 CST)
    - Re: [AMBER] how many processors for parallel test michael bane (Thu Jan 08 2009 - 07:56:59 CST)
[AMBER] Can we use Amber? Casey,Richard (Thu Jan 08 2009 - 11:16:50 CST)
[AMBER] mairun wl2290_at_columbia.edu (Thu Jan 08 2009 - 11:30:05 CST)
- RE: [AMBER] mairun Ross Walker (Thu Jan 08 2009 - 12:25:26 CST)
  - RE: [AMBER] mairun wl2290_at_columbia.edu (Thu Jan 08 2009 - 16:33:52 CST)
    - RE: [AMBER] mairun Ross Walker (Thu Jan 08 2009 - 16:51:49 CST)
    - RE: [AMBER] mairun wl2290_at_columbia.edu (Thu Jan 08 2009 - 17:11:56 CST)
[AMBER] Can we use AMBER? Casey,Richard (Thu Jan 08 2009 - 11:25:57 CST)
- RE: [AMBER] Can we use AMBER? Ross Walker (Thu Jan 08 2009 - 12:47:18 CST)
[AMBER] lone pairs on CYX and MET Beale, John (Thu Jan 08 2009 - 12:08:42 CST)
- RE: [AMBER] lone pairs on CYX and MET Ross Walker (Thu Jan 08 2009 - 12:17:52 CST)
[AMBER] Need help with point to plane distance calculation in nab M. L. Dodson (Thu Jan 08 2009 - 12:39:16 CST)
- Re: [AMBER] Need help with point to plane distance calculation in nab IN SUK JOUNG (Thu Jan 08 2009 - 13:00:20 CST)
  - Re: [AMBER] Need help with point to plane distance calculation in nab M. L. Dodson (Thu Jan 08 2009 - 13:16:51 CST)
    - Re: [AMBER] Need help with point to plane distance calculation in nab IN SUK JOUNG (Thu Jan 08 2009 - 13:41:09 CST)
    - Re: [AMBER] Need help with point to plane distance calculation in nab M. L. Dodson (Thu Jan 08 2009 - 13:54:15 CST)
RE: [AMBER] mpirun Ross Walker (Thu Jan 08 2009 - 17:28:12 CST)
[AMBER] force-field for cyclic oligosaccharide using leap Madhurima Jana (Thu Jan 08 2009 - 22:50:18 CST)
- [AMBER] force-field for cyclic oligosaccharide using leap Madhurima Jana (Sun Jan 11 2009 - 22:21:23 CST)
[AMBER] NAB entropy calcualtion chaitanya koppisetty (Fri Jan 09 2009 - 03:01:13 CST)
- Re: [AMBER] NAB entropy calcualtion Andreas Svrcek-Seiler (Fri Jan 09 2009 - 03:28:48 CST)
- Re: [AMBER] NAB entropy calcualtion David A. Case (Fri Jan 09 2009 - 07:13:32 CST)
[AMBER] ambpdb is changing atom names, a feature or bug? Markus Kaukonen (Fri Jan 09 2009 - 06:55:41 CST)
- Re: [AMBER] ambpdb is changing atom names, a feature or bug? David A. Case (Fri Jan 09 2009 - 07:01:54 CST)
[AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai (Fri Jan 09 2009 - 10:27:56 CST)
- Re: [AMBER] problem building AmberTools/sleap on AIX Wei Zhang (Fri Jan 09 2009 - 10:37:43 CST)
  - Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai (Fri Jan 09 2009 - 10:46:59 CST)
- Re: [AMBER] problem building AmberTools/sleap on AIX Bill Ross (Fri Jan 09 2009 - 11:45:55 CST)
  - Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai (Fri Jan 09 2009 - 15:49:17 CST)
[AMBER] "bad atom type" Akansha Saxena (Fri Jan 09 2009 - 11:15:11 CST)
Re: [AMBER] ambpdb is changing atom names, a feature or bug? Bill Ross (Fri Jan 09 2009 - 11:53:23 CST)
- Re: [AMBER] ambpdb is changing atom names, a feature or bug? David A. Case (Fri Jan 09 2009 - 12:58:20 CST)
- Re: Re: [AMBER] ambpdb is changing atom names, a feature or bug? Ye Mei (Sat Jan 10 2009 - 02:03:10 CST)
  - Re: Re: [AMBER] ambpdb is changing atom names, a feature or bug? David A. Case (Sat Jan 10 2009 - 10:02:53 CST)
[AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Fri Jan 09 2009 - 15:07:13 CST)
- Re: [AMBER] number-of-EPS-exceeds-MAXESP FyD (Sat Jan 10 2009 - 02:26:13 CST)
  - Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Sat Jan 10 2009 - 09:27:08 CST)
    - Re: [AMBER] number-of-EPS-exceeds-MAXESP FyD (Sun Jan 11 2009 - 01:00:40 CST)
    - Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Sun Jan 11 2009 - 02:01:07 CST)
- Re: [AMBER] number-of-EPS-exceeds-MAXESP FyD (Mon Jan 12 2009 - 01:43:48 CST)
  - Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Mon Jan 12 2009 - 01:57:50 CST)
    - Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Sat Jan 17 2009 - 04:41:22 CST)
[AMBER] implicit and explicit simulation: salt effect Catein Catherine (Fri Jan 09 2009 - 21:03:35 CST)
- Re: [AMBER] implicit and explicit simulation: salt effect David Watson (Fri Jan 09 2009 - 21:49:48 CST)
  - Re: [AMBER] implicit and explicit simulation: salt effect David LeBard (Fri Jan 09 2009 - 22:23:24 CST)
    - Re: [AMBER] implicit and explicit simulation: salt effect David A. Case (Sat Jan 10 2009 - 10:26:45 CST)
- Re: [AMBER] implicit and explicit simulation: salt effect David A. Case (Sat Jan 10 2009 - 10:23:08 CST)
[AMBER] mm-GBSA from implicit Catein Catherine (Fri Jan 09 2009 - 21:13:28 CST)
- Re: [AMBER] mm-GBSA from implicit Carlos Simmerling (Sat Jan 10 2009 - 07:25:10 CST)
[AMBER] Off topic. Hardware problem Francesco Pietra (Sat Jan 10 2009 - 02:26:55 CST)
[AMBER] Can't reproduce RESP charges Sanghwa Han (Sun Jan 11 2009 - 23:57:15 CST)
- Re: [AMBER] Can't reproduce RESP charges FyD (Tue Jan 13 2009 - 05:52:13 CST)
[AMBER] Amber 9 installation problem on Ubuntu drugdesign (Mon Jan 12 2009 - 00:26:34 CST)
- Re: [AMBER] Amber 9 installation problem on Ubuntu David A. Case (Mon Jan 12 2009 - 06:01:31 CST)
[AMBER] Release of the R.E.D.-III.1 tools FyD (Mon Jan 12 2009 - 05:59:14 CST)
[AMBER] Parallelepiped periodic box Ian Streeter (Mon Jan 12 2009 - 09:57:55 CST)
- Re: [AMBER] Parallelepiped periodic box David A. Case (Fri Jan 16 2009 - 13:50:32 CST)
[AMBER] Writing out trajectory in NAB xxxzzzyyy xxxzzzyyy (Mon Jan 12 2009 - 10:43:33 CST)
- Re: [AMBER] Writing out trajectory in NAB David A. Case (Mon Jan 12 2009 - 11:22:58 CST)
[AMBER] crystal waters Carmen Domene (Mon Jan 12 2009 - 14:04:24 CST)
- Re: [AMBER] crystal waters steinbrt_at_rci.rutgers.edu (Mon Jan 12 2009 - 14:16:25 CST)
  - Re: [AMBER] crystal waters Carmen Domene (Mon Jan 12 2009 - 14:32:28 CST)
    - Re: [AMBER] crystal waters steinbrt_at_rci.rutgers.edu (Mon Jan 12 2009 - 14:37:34 CST)
[AMBER] multisander error Justine Condo (Mon Jan 12 2009 - 16:03:37 CST)
- Re: [AMBER] multisander error David Watson (Mon Jan 12 2009 - 16:15:26 CST)
- RE: [AMBER] multisander error Ross Walker (Mon Jan 12 2009 - 16:20:06 CST)
  - Re: [AMBER] multisander error Justine Condo (Mon Jan 12 2009 - 16:32:31 CST)
  - Re: [AMBER] multisander error Justine Condo (Mon Jan 12 2009 - 16:39:44 CST)
    - RE: [AMBER] multisander error Ross Walker (Mon Jan 12 2009 - 16:51:48 CST)
    - Re: [AMBER] multisander error Justine Condo (Mon Jan 12 2009 - 17:01:41 CST)
[AMBER] error in sander (Amber10) archana sonawani (Tue Jan 13 2009 - 02:21:09 CST)
[AMBER] errorin sander---Amber10 archana sonawani (Tue Jan 13 2009 - 03:27:43 CST)
- Re: [AMBER] errorin sander---Amber10 David A. Case (Tue Jan 13 2009 - 07:22:36 CST)
[AMBER] amber9 in fedora10 Bala subramanian (Tue Jan 13 2009 - 11:51:49 CST)
- Re: [AMBER] amber9 in fedora10 Mark Williamson (Tue Jan 13 2009 - 11:56:31 CST)
- RE: [AMBER] amber9 in fedora10 Ross Walker (Tue Jan 13 2009 - 12:00:33 CST)
  - Re: [AMBER] amber9 in fedora10 Bala subramanian (Tue Jan 13 2009 - 12:16:19 CST)
    - Re: [AMBER] amber9 in fedora10 Eric (Tue Jan 13 2009 - 12:28:33 CST)
  - [AMBER] PTRAJ: solvent accessible surface area Catein Catherine (Wed Jan 14 2009 - 01:32:15 CST)
    - Re: [AMBER] PTRAJ: solvent accessible surface area steinbrt_at_rci.rutgers.edu (Wed Jan 14 2009 - 08:59:19 CST)
    - Re: [AMBER] PTRAJ: solvent accessible surface area Carlos Simmerling (Wed Jan 14 2009 - 09:00:59 CST)
[AMBER] principal component vector onto C-alpha Carra, Claudio (JSC-SK)[USRA] (Tue Jan 13 2009 - 14:52:31 CST)
- Re: [AMBER] principal component vector onto C-alpha S.Sundar Raman (Tue Jan 13 2009 - 16:46:20 CST)
[AMBER] Divcon or Mopac Cen Gao (Tue Jan 13 2009 - 17:54:33 CST)
- Re: [AMBER] Divcon or Mopac Martin Peters (Wed Jan 14 2009 - 03:01:12 CST)
[AMBER] ptraj, CHARMM PSF and CMAP Hannes Loeffler (Wed Jan 14 2009 - 03:45:07 CST)
- RE: [AMBER] ptraj, CHARMM PSF and CMAP Ross Walker (Wed Jan 14 2009 - 10:46:17 CST)
[AMBER] charges in topology file vallespardojl_at_chem.leidenuniv.nl (Wed Jan 14 2009 - 04:33:35 CST)
- Re: [AMBER] charges in topology file Carlos Simmerling (Wed Jan 14 2009 - 05:24:52 CST)
- Re: [AMBER] charges in topology file Jeffrey (Fri Jul 10 2009 - 11:20:01 CDT)
[AMBER] reaction coordinates Rausch, Felix (Wed Jan 14 2009 - 05:54:57 CST)
- Re: [AMBER] reaction coordinates David A. Case (Wed Jan 14 2009 - 07:00:59 CST)
  - RE: [AMBER] reaction coordinates Catein Catherine (Wed Jan 14 2009 - 23:25:31 CST)
[AMBER] antechamber cation failure Rausch, Felix (Wed Jan 14 2009 - 07:32:04 CST)
- RE: [AMBER] antechamber cation failure Ross Walker (Wed Jan 14 2009 - 11:45:43 CST)
[AMBER] NPT md with PME method for a water box Jeffrey (Wed Jan 14 2009 - 08:41:24 CST)
- RE: [AMBER] NPT md with PME method for a water box Ross Walker (Wed Jan 14 2009 - 12:07:13 CST)
[AMBER] molecular mechanic minimisation with amber momo momo (Wed Jan 14 2009 - 08:58:47 CST)
- RE: [AMBER] molecular mechanic minimisation with amber Ross Walker (Wed Jan 14 2009 - 11:56:23 CST)
[AMBER] Dipole command in ptraj musa özboyacý (Wed Jan 14 2009 - 09:41:07 CST)
[AMBER] pmemd | Compilation problem with ifort and mvapich environment fohm fohm (Wed Jan 14 2009 - 11:23:50 CST)
- RE: [AMBER] pmemd | Compilation problem with ifort and mvapich environment Ross Walker (Wed Jan 14 2009 - 11:53:20 CST)
[AMBER] bad energy??!! momo momo (Wed Jan 14 2009 - 13:19:20 CST)
- RE: [AMBER] bad energy??!! Ross Walker (Wed Jan 14 2009 - 13:40:24 CST)
[AMBER] Postdoc Position Available at SDSC/UCSD Ross Walker (Wed Jan 14 2009 - 14:35:52 CST)
[AMBER] Dipole command in ptraj musa özboyacý (Wed Jan 14 2009 - 17:15:26 CST)
[AMBER] xmgrace and plotting time evolution of a defined variable Naser Alijabbari (Wed Jan 14 2009 - 18:20:31 CST)
- Re: [AMBER] xmgrace and plotting time evolution of a defined variable Mark Williamson (Wed Jan 14 2009 - 18:38:17 CST)
[AMBER] Error in xleap archana sonawani (Thu Jan 15 2009 - 01:39:16 CST)
- RE: [AMBER] Error in xleap Ross Walker (Thu Jan 15 2009 - 10:01:20 CST)
[AMBER] Using a restart file Simone Swift (Thu Jan 15 2009 - 10:40:38 CST)
- Re: [AMBER] Using a restart file Carlos Simmerling (Thu Jan 15 2009 - 10:45:27 CST)
- RE: [AMBER] Using a restart file Ross Walker (Thu Jan 15 2009 - 10:52:44 CST)
[AMBER] Ligand Diffusion Studies? Jason A. Ford-Green (Thu Jan 15 2009 - 11:42:03 CST)
[AMBER] restraint of REMD z g (Thu Jan 15 2009 - 20:51:46 CST)
- Re: [AMBER] restraint of REMD Carlos Simmerling (Fri Jan 16 2009 - 05:57:29 CST)
[AMBER] sander not working archana sonawani (Thu Jan 15 2009 - 23:52:48 CST)
- Re: [AMBER] sander not working David A. Case (Fri Jan 16 2009 - 08:58:50 CST)
- Re: [AMBER] sander not working Carlos Simmerling (Fri Jan 16 2009 - 09:01:34 CST)
[AMBER] nab conjgrad min problem Jeremy Harris (Fri Jan 16 2009 - 09:11:12 CST)
- Re: [AMBER] nab conjgrad min problem David A. Case (Fri Jan 16 2009 - 09:33:01 CST)
  - Re: [AMBER] nab conjgrad min problem Jeremy Harris (Mon Jan 19 2009 - 09:00:30 CST)
[AMBER] RE: Tutorial 5 Ross Walker (Fri Jan 16 2009 - 11:10:51 CST)
- Re: [AMBER] RE: Tutorial 5 George Tzotzos (Fri Jan 16 2009 - 14:31:11 CST)
[AMBER] (no subject) Lake, Thomas (Fri Jan 16 2009 - 11:38:09 CST)
- Re: [AMBER] (no subject) Carlos Simmerling (Fri Jan 16 2009 - 11:43:26 CST)
  - Re: [AMBER] (no subject) Jenny Iskrenova (Fri Jan 16 2009 - 12:42:08 CST)
[AMBER] Heat and Equilibrate Hybrid GB solvent? Jason A. Ford-Green (Fri Jan 16 2009 - 15:14:41 CST)
- Re: [AMBER] Heat and Equilibrate Hybrid GB solvent? Carlos Simmerling (Fri Jan 16 2009 - 15:21:27 CST)
[AMBER] Use of Amber in distributed calculations drugdesign (Sat Jan 17 2009 - 01:33:55 CST)
- Re: [AMBER] Use of Amber in distributed calculations M. L. Dodson (Sat Jan 17 2009 - 07:48:42 CST)
  - Re: [AMBER] Use of Amber in distributed calculations M. L. Dodson (Sat Jan 17 2009 - 08:01:36 CST)
[AMBER] To stop the AMBER's list Furia Gargano (Sat Jan 17 2009 - 11:59:48 CST)
[AMBER] to remove AMBER list Furia Gargano (Sat Jan 17 2009 - 12:02:26 CST)
- RE: [AMBER] to remove AMBER list Ross Walker (Sat Jan 17 2009 - 15:32:19 CST)
[AMBER] AMBER efficiency: Intel vs. AMD Swarup Gupta (Sun Jan 18 2009 - 19:43:32 CST)
- Re: [AMBER] AMBER efficiency: Intel vs. AMD Ye MEI (Sun Jan 18 2009 - 20:20:47 CST)
- RE: [AMBER] AMBER efficiency: Intel vs. AMD Ross Walker (Mon Jan 19 2009 - 09:39:33 CST)
[AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent" Jagadeesh, M.N., Ph.D. (Mon Jan 19 2009 - 03:03:39 CST)
- Re: [AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent" Carlos Simmerling (Tue Jan 20 2009 - 08:33:55 CST)
[AMBER] RESP charges for Fe in heme Carina Backtorp (Mon Jan 19 2009 - 07:48:11 CST)
[AMBER] Atom types George Tzotzos (Mon Jan 19 2009 - 08:04:09 CST)
- RE: [AMBER] Atom types Ross Walker (Mon Jan 19 2009 - 09:46:10 CST)
- RE: [AMBER] Atom types George Tzotzos (Mon Jan 19 2009 - 12:02:42 CST)
[AMBER] errors on REMD z g (Mon Jan 19 2009 - 20:41:35 CST)
- Re: [AMBER] errors on REMD Carlos Simmerling (Tue Jan 20 2009 - 05:02:06 CST)
  - Re: [AMBER] errors on REMD z g (Tue Jan 20 2009 - 07:39:12 CST)
[AMBER] analysis Adrien Delmont (Tue Jan 20 2009 - 11:03:16 CST)
[AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Marek Malý (Tue Jan 20 2009 - 12:24:55 CST)
- RE: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Niel Henriksen (Tue Jan 20 2009 - 14:49:38 CST)
- Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. David A. Case (Tue Jan 20 2009 - 14:53:48 CST)
  - [AMBER] MD vs scattering Chih-Ying Lin (Tue Jan 20 2009 - 15:10:47 CST)
    - RE: [AMBER] MD vs scattering Ross Walker (Tue Jan 20 2009 - 15:18:26 CST)
    - Re: RE: [AMBER] MD vs scattering Chih-Ying Lin (Tue Jan 20 2009 - 15:26:49 CST)
  - Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Marek Malý (Tue Jan 20 2009 - 20:48:03 CST)
[AMBER] solvent mixture iccy liu (Tue Jan 20 2009 - 16:08:34 CST)
- Re: [AMBER] solvent mixture Gustavo Seabra (Sat Jan 24 2009 - 20:44:31 CST)
[AMBER] How to calculate cavity volume from MD structures? ben rodriguez (Tue Jan 20 2009 - 16:21:43 CST)
- Re: [AMBER] How to calculate cavity volume from MD structures? Jason A. Ford-Green (Wed Jan 21 2009 - 09:39:57 CST)
[AMBER] prot-DNA simulation deepti nayar (Wed Jan 21 2009 - 05:16:09 CST)
- Re: [AMBER] prot-DNA simulation Thomas Cheatham III (Wed Jan 21 2009 - 15:55:52 CST)
[AMBER] AMBER External keyword Mahmoud A. A. Ibrahim (Wed Jan 21 2009 - 09:59:33 CST)
- Re: [AMBER] AMBER External keyword Gustavo Seabra (Sat Jan 24 2009 - 20:32:10 CST)
[AMBER] how to use those water models off the list in amber? GZ Zhang (Wed Jan 21 2009 - 15:39:50 CST)
- Re: [AMBER] how to use those water models off the list in amber? Lauren Wickstrom (Wed Jan 21 2009 - 17:58:22 CST)
- Re: [AMBER] how to use those water models off the list in amber? David A. Case (Thu Jan 22 2009 - 07:29:41 CST)
  - Re: [AMBER] how to use those water models off the list in amber? GZ Zhang (Thu Jan 22 2009 - 14:47:02 CST)
[AMBER] reg . parallel run balaji nagarajan (Wed Jan 21 2009 - 23:34:03 CST)
- RE: [AMBER] reg . parallel run Ross Walker (Thu Jan 22 2009 - 09:52:55 CST)
[AMBER] (no subject) Lake, Thomas (Thu Jan 22 2009 - 07:43:59 CST)
- [AMBER] restraining atoms neville forlemu (Thu Jan 22 2009 - 08:53:48 CST)
  - Re: [AMBER] restraining atoms Carlos Simmerling (Thu Jan 22 2009 - 08:55:35 CST)
- RE: [AMBER] (no subject) Ross Walker (Thu Jan 22 2009 - 09:46:56 CST)
[AMBER] MM - PBSA problem musa özboyacý (Thu Jan 22 2009 - 11:06:54 CST)
- RE: [AMBER] MM - PBSA problem Ray Luo (Thu Jan 22 2009 - 11:31:53 CST)
  - Re: [AMBER] MM - PBSA problem musa özboyacý (Thu Jan 22 2009 - 13:52:10 CST)
    - Re: [AMBER] MM - PBSA problem Cenk \(Jenk\) Andac (Thu Jan 22 2009 - 16:00:13 CST)
- RE: [AMBER] MM - PBSA problem Niel Henriksen (Thu Jan 22 2009 - 18:52:09 CST)
  - Re: [AMBER] MM - PBSA problem musa özboyacý (Fri Jan 23 2009 - 07:14:05 CST)
[AMBER] non-natural amino acids Arturas Ziemys (Thu Jan 22 2009 - 11:32:11 CST)
- Re: [AMBER] non-natural amino acids FyD (Thu Jan 22 2009 - 17:25:31 CST)
[AMBER] reg.parallel run error balaji nagarajan (Thu Jan 22 2009 - 12:41:25 CST)
- RE: [AMBER] reg.parallel run error Ross Walker (Thu Jan 22 2009 - 14:06:33 CST)
[AMBER] REM_hybrid test fails on AIX Shan-ho Tsai (Thu Jan 22 2009 - 14:28:04 CST)
- Re: [AMBER] REM_hybrid test fails on AIX Shan-ho Tsai (Thu Feb 05 2009 - 10:44:43 CST)
[AMBER] reg.error in parallel run balaji nagarajan (Fri Jan 23 2009 - 04:05:21 CST)
- RE: [AMBER] reg.error in parallel run Ross Walker (Fri Jan 23 2009 - 09:52:20 CST)
[AMBER] charge derivation for ATP molecule using antechamber prachi munjal (Fri Jan 23 2009 - 07:19:27 CST)
- Re: [AMBER] charge derivation for ATP molecule using antechamber David A. Case (Fri Jan 23 2009 - 10:51:49 CST)
[AMBER] RE: errors on remd Ross Walker (Fri Jan 23 2009 - 10:38:06 CST)
Re: [AMBER] "Could not find bond parameter" George Tzotzos (Fri Jan 23 2009 - 12:16:34 CST)
- RE: [AMBER] "Could not find bond parameter" Ross Walker (Fri Jan 23 2009 - 12:29:46 CST)
[AMBER] reg.parallel.run error balaji nagarajan (Fri Jan 23 2009 - 19:59:21 CST)
- RE: [AMBER] reg.parallel.run error Ross Walker (Sat Jan 24 2009 - 00:05:50 CST)
[AMBER] error on open distatance restraint gmail (Fri Jan 23 2009 - 20:58:27 CST)
- Re: [AMBER] error on open distatance restraint David A. Case (Fri Jan 23 2009 - 21:18:17 CST)
  - Re: [AMBER] error on open distatance restraint xiaonan zhang (Sat Jan 24 2009 - 21:56:02 CST)
[AMBER] reg.parallel.run.error balaji nagarajan (Sat Jan 24 2009 - 09:09:49 CST)
[AMBER] Very weird topology problem ranqi zhu (Sat Jan 24 2009 - 15:14:24 CST)
- Re: [AMBER] Very weird topology problem Peter Gannett (Sat Jan 24 2009 - 17:17:26 CST)
[AMBER] AmberTools and ptraj clustering on Mac OS X David Watson (Sat Jan 24 2009 - 15:41:04 CST)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 05:56:12 CST)
- Re: [AMBER] xleap problem David A. Case (Sun Jan 25 2009 - 07:57:41 CST)
  - Re: [AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 10:02:50 CST)
[AMBER] RE:xleap problem oguz gurbulak (Sun Jan 25 2009 - 10:08:26 CST)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 10:27:48 CST)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 10:34:39 CST)
- Re: [AMBER] xleap problem David A. Case (Sun Jan 25 2009 - 17:30:47 CST)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 05:49:28 CST)
[AMBER] deduce correlation from covariance matrix Yi Mao (Sun Jan 25 2009 - 15:01:05 CST)
[AMBER] using binary trajectories from NAMD in PTRAJ karthik s (Mon Jan 26 2009 - 01:11:29 CST)
- RE: [AMBER] using binary trajectories from NAMD in PTRAJ Wei Huang (Mon Jan 26 2009 - 08:41:22 CST)
  - Re: [AMBER] using binary trajectories from NAMD in PTRAJ karthik s (Tue Jan 27 2009 - 00:49:13 CST)
[AMBER] thioglycoside Alexander Schierholt (Mon Jan 26 2009 - 08:46:28 CST)
- Re: [AMBER] thioglycoside FyD (Mon Jan 26 2009 - 09:07:37 CST)
- Re: [AMBER] thioglycoside Lachele Foley (Lists) (Mon Jan 26 2009 - 09:36:26 CST)
Re: [AMBER] Antechamber Connectivity George Tzotzos (Mon Jan 26 2009 - 12:23:58 CST)
- Re: [AMBER] Antechamber Connectivity David Watson (Mon Jan 26 2009 - 13:59:58 CST)
[AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 12:54:07 CST)
- Re: [AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 13:15:33 CST)
  - Re: [AMBER] antechamber : missed atoms David A. Case (Tue Jan 27 2009 - 09:23:27 CST)
- Re: [AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 13:20:52 CST)
  - Re: [AMBER] antechamber : missed atoms Sean Johnston (Mon Jan 26 2009 - 13:40:59 CST)
- Re: [AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 14:22:14 CST)
[AMBER] RE:xleap problem oguz gurbulak (Mon Jan 26 2009 - 13:48:11 CST)
- Re: [AMBER] RE:xleap problem M. L. Dodson (Mon Jan 26 2009 - 14:47:26 CST)
  - Re: [AMBER] RE:xleap problem oguz gurbulak (Mon Jan 26 2009 - 15:40:22 CST)
[AMBER] atom types deepti nayar (Tue Jan 27 2009 - 03:47:12 CST)
- Re: [AMBER] atom types David A. Case (Tue Jan 27 2009 - 09:13:30 CST)
[AMBER] reg: targeted molecular dynamics balaji nagarajan (Tue Jan 27 2009 - 07:02:03 CST)
- Re: [AMBER] reg: targeted molecular dynamics Carlos Simmerling (Tue Jan 27 2009 - 07:04:57 CST)
[AMBER] Rosetta Academic Training Workshop Nir London (Tue Jan 27 2009 - 07:07:24 CST)
[AMBER] reg.Targeted molecular dynamics balaji nagarajan (Tue Jan 27 2009 - 07:56:54 CST)
[AMBER] reg.Targeted molecular dynamics balaji nagarajan (Tue Jan 27 2009 - 07:57:01 CST)
- Re: [AMBER] reg.Targeted molecular dynamics Carlos Simmerling (Wed Jan 28 2009 - 12:01:43 CST)
Re: [AMBER] Antechamber ligand prep George Tzotzos (Tue Jan 27 2009 - 08:48:11 CST)
- Re: [AMBER] Antechamber ligand prep David A. Case (Tue Jan 27 2009 - 08:59:47 CST)
  - Re: [AMBER] Antechamber ligand prep George Tzotzos (Tue Jan 27 2009 - 09:24:30 CST)
[AMBER] NOTICE: File size limits on AMBER reflector Ross Walker (Tue Jan 27 2009 - 10:35:50 CST)
[AMBER] distance restraint and SHAKE Michael J Yonkunas (Tue Jan 27 2009 - 11:39:56 CST)
- Re: [AMBER] distance restraint and SHAKE Thomas Cheatham III (Tue Jan 27 2009 - 12:16:30 CST)
Re: [AMBER] Building atom and angle parameters George Tzotzos (Tue Jan 27 2009 - 12:24:52 CST)
[AMBER] topology file for GLY with amino and carboxyl group? Jose Borreguero (Tue Jan 27 2009 - 12:57:45 CST)
- Re: [AMBER] topology file for GLY with amino and carboxyl group? FyD (Tue Jan 27 2009 - 14:02:14 CST)
[AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Tue Jan 27 2009 - 16:40:49 CST)
- Re: [AMBER] large resp charges for non-natural amino acid FyD (Wed Jan 28 2009 - 22:04:11 CST)
  - Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Thu Jan 29 2009 - 09:10:50 CST)
- Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Sat Jan 31 2009 - 11:03:09 CST)
- Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Sat Jan 31 2009 - 11:03:44 CST)
[AMBER] PhD position in Computational Structural Biology at Cambridge, UK Swanand Gore (Wed Jan 28 2009 - 04:31:16 CST)
[AMBER] GAFF conjugated ring system dihedrals Floris Buelens (Wed Jan 28 2009 - 06:04:55 CST)
- Re: [AMBER] GAFF conjugated ring system dihedrals David A. Case (Thu Jan 29 2009 - 12:37:24 CST)
[AMBER] Watercap... some querries Waqas Nasir (Wed Jan 28 2009 - 08:54:00 CST)
- Re: [AMBER] Watercap... some querries David A. Case (Wed Jan 28 2009 - 09:01:46 CST)
  - Re: [AMBER] Watercap... some querries Waqas Nasir (Wed Jan 28 2009 - 09:10:48 CST)
  - Re: [AMBER] Watercap... some querries Robert Duke (Wed Jan 28 2009 - 12:46:02 CST)
[AMBER] generating top file using antechmaber sarvin moghaddam (Wed Jan 28 2009 - 13:49:20 CST)
- Re: [AMBER] generating top file using antechmaber Wei Zhang (Wed Jan 28 2009 - 14:12:20 CST)
  - Re: [AMBER] generating top file using antechmaber sarvin moghaddam (Thu Jan 29 2009 - 09:24:50 CST)
    - Re: [AMBER] generating top file using antechmaber Wei Zhang (Thu Jan 29 2009 - 10:26:22 CST)
- Re: [AMBER] generating top file using antechmaber Wei Zhang (Wed Jan 28 2009 - 14:23:21 CST)
  - Re: [AMBER] generating top file using antechmaber sarvin moghaddam (Wed Jan 28 2009 - 14:33:00 CST)
    - Re: [AMBER] generating top file using antechmaber David A. Case (Thu Jan 29 2009 - 06:51:56 CST)
[AMBER] Compilation and usage of NAB in parallel ? Marek Malý (Wed Jan 28 2009 - 16:25:24 CST)
- Re: [AMBER] Compilation and usage of NAB in parallel ? David A. Case (Thu Jan 29 2009 - 07:22:08 CST)
  - Re: [AMBER] Compilation and usage of NAB in parallel ? Marek Malý (Fri Jan 30 2009 - 08:59:07 CST)
    - Re: [AMBER] Compilation and usage of NAB in parallel ? David A. Case (Fri Jan 30 2009 - 09:51:31 CST)
    - Re: [AMBER] Compilation and usage of NAB in parallel ? Marek Malý (Fri Jan 30 2009 - 10:01:06 CST)
[AMBER] atomic charge m m (Thu Jan 29 2009 - 02:08:47 CST)
- Re: [AMBER] atomic charge Barbault Florent (Thu Jan 29 2009 - 02:24:48 CST)
[AMBER] Problem in pb simulation, PB_Bomb Waqas Nasir (Thu Jan 29 2009 - 03:08:22 CST)
[AMBER] Dr. Ramesh here kureeckal ramesh (Thu Jan 29 2009 - 04:41:10 CST)
- Re: [AMBER] Dr. Ramesh here rpaduri_at_chem.wayne.edu (Thu Jan 29 2009 - 11:22:20 CST)
  - Re: [AMBER] Dr. Ramesh here kureeckal ramesh (Thu Jan 29 2009 - 19:41:17 CST)
  - Re: [AMBER] Dr. Ramesh here kureeckal ramesh (Thu Jan 29 2009 - 21:18:33 CST)
    - Re: [AMBER] Dr. Ramesh here David A. Case (Fri Jan 30 2009 - 10:08:43 CST)
    - Re: [AMBER] Dr. Ramesh here kureeckal ramesh (Mon Feb 02 2009 - 08:22:51 CST)
[AMBER] Atome Type Mahmoud A. A. Ibrahim (Thu Jan 29 2009 - 04:59:42 CST)
- Re: [AMBER] Atome Type David A. Case (Thu Jan 29 2009 - 07:08:09 CST)
[AMBER] Installation error - Amber10 Ananda Rama Krishnan Selvaraj (Thu Jan 29 2009 - 05:47:44 CST)
- Re: [AMBER] Installation error - Amber10 Andreas Svrcek-Seiler (Thu Jan 29 2009 - 05:52:44 CST)
  - Re: [AMBER] Installation error - Amber10 David A. Case (Thu Jan 29 2009 - 12:33:33 CST)
[AMBER] Problem in watercap simulation, PB_Bomb Waqas Nasir (Thu Jan 29 2009 - 08:21:20 CST)
- RE: [AMBER] Problem in watercap simulation, PB_Bomb Ray Luo (Thu Jan 29 2009 - 11:45:33 CST)
[AMBER] Alpha helix plot Beale, John (Thu Jan 29 2009 - 14:10:11 CST)
- Re: [AMBER] Alpha helix plot Carlos Simmerling (Fri Jan 30 2009 - 16:11:10 CST)
[AMBER] failure to run antechamber with amber 10 Francesco Pietra (Thu Jan 29 2009 - 16:29:18 CST)
- Re: [AMBER] failure to run antechamber with amber 10 David A. Case (Thu Jan 29 2009 - 16:45:53 CST)
  - Re: [AMBER] failure to run antechamber with amber 10 Francesco Pietra (Fri Jan 30 2009 - 02:04:33 CST)
- Re: [AMBER] failure to run antechamber with amber 10 George Tzotzos (Thu Jan 29 2009 - 16:48:50 CST)
[AMBER] AmberTools 1.2 James W. Caldwell (Thu Jan 29 2009 - 18:04:36 CST)
- Re: [AMBER] AmberTools 1.2 David A. Case (Fri Jan 30 2009 - 06:04:41 CST)
[AMBER] adding MG2 problem balaji nagarajan (Fri Jan 30 2009 - 03:45:58 CST)
- Re: [AMBER] adding MG2 problem Scott Brozell (Tue Feb 03 2009 - 13:09:32 CST)
  - RE: [AMBER] adding MG2 problem Rausch, Felix (Wed Feb 04 2009 - 07:04:51 CST)
[AMBER] Xleap - solvatebox - counterions Arnaud (Fri Jan 30 2009 - 04:44:58 CST)
- Re: [AMBER] Xleap - solvatebox - counterions David A. Case (Fri Jan 30 2009 - 10:04:23 CST)
  - RE: [AMBER] Xleap - solvatebox - counterions amirhossein taghavi (Sat Jan 31 2009 - 11:34:10 CST)
[AMBER] help momo momo (Fri Jan 30 2009 - 06:35:22 CST)
- RE: [AMBER] help Ross Walker (Fri Jan 30 2009 - 07:42:33 CST)
[AMBER] Amber top file to Charmm top file sarvin moghaddam (Fri Jan 30 2009 - 08:48:44 CST)
[AMBER] REMD fixed atoms Maxime Louet (Fri Jan 30 2009 - 11:26:08 CST)
- Re: [AMBER] REMD fixed atoms Carlos Simmerling (Sun Feb 01 2009 - 12:00:33 CST)
Re: [AMBER] Xleap - solvatebox - counterions Bill Ross (Fri Jan 30 2009 - 12:40:07 CST)
[AMBER] thermo, entropy by quasiharmonic method Carra, Claudio (JSC-SK)[USRA] (Fri Jan 30 2009 - 15:35:37 CST)
- Re: [AMBER] thermo, entropy by quasiharmonic method David A. Case (Fri Jan 30 2009 - 17:40:38 CST)
[AMBER] RE: Tutorial 5 Ross Walker (Fri Jan 30 2009 - 19:32:03 CST)
- Re: [AMBER] RE: Tutorial 5 George Tzotzos (Sun Feb 01 2009 - 15:04:36 CST)
[AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran (Sat Jan 31 2009 - 12:39:14 CST)
- Re: [AMBER] Test run on Solaris 10 X 86 David A. Case (Sat Jan 31 2009 - 20:49:22 CST)
  - [AMBER] Citing AMBER Tools... Aydin, Cihan (Sat Jan 31 2009 - 23:08:36 CST)
    - Re: [AMBER] Citing AMBER Tools... David A. Case (Thu Feb 05 2009 - 09:44:37 CST)
- Re: [AMBER] Test run on Solaris 10 X 86 Atro Tossavainen (Sun Feb 01 2009 - 01:10:30 CST)
  - Re: [AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran (Mon Feb 02 2009 - 13:16:32 CST)
[AMBER] Question on heating for homology based model. drugdesign (Sat Jan 31 2009 - 12:43:06 CST)
- Re: [AMBER] Question on heating for homology based model. Carlos Simmerling (Sun Feb 01 2009 - 11:47:02 CST)
[AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? liu junjun (Sun Feb 01 2009 - 01:51:39 CST)
- Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? Carlos Simmerling (Sun Feb 01 2009 - 11:55:54 CST)
- Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? David A. Case (Sun Feb 01 2009 - 12:35:03 CST)
  - Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? liu junjun (Mon Feb 02 2009 - 10:25:41 CST)
[AMBER] the output files oguz gurbulak (Sun Feb 01 2009 - 05:13:02 CST)
- Re: [AMBER] the output files Carlos Simmerling (Sun Feb 01 2009 - 12:11:51 CST)
  - Re: [AMBER] the output files oguz gurbulak (Mon Feb 09 2009 - 07:03:47 CST)
[AMBER] strip frames from crd file aneesh cna (Mon Feb 02 2009 - 03:33:16 CST)
- Re: [AMBER] strip frames from crd file Carlos Simmerling (Mon Feb 02 2009 - 06:12:27 CST)
[AMBER] strip frames from crd file aneesh cna (Mon Feb 02 2009 - 03:35:11 CST)
[AMBER] md simulation on parallel PMEMD oguz gurbulak (Mon Feb 02 2009 - 07:32:31 CST)
- Re: [AMBER] md simulation on parallel PMEMD David A. Case (Mon Feb 02 2009 - 07:54:58 CST)
- Re: [AMBER] md simulation on parallel PMEMD Carlos Simmerling (Mon Feb 02 2009 - 07:55:44 CST)
- Re: [AMBER] md simulation on parallel PMEMD Robert Duke (Mon Feb 02 2009 - 08:03:59 CST)
[AMBER] precision in the trajectory files Jenny Iskrenova (Mon Feb 02 2009 - 08:43:38 CST)
- Re: [AMBER] precision in the trajectory files Adrian Roitberg (Mon Feb 02 2009 - 08:46:49 CST)
- Re: [AMBER] precision in the trajectory files David A. Case (Mon Feb 02 2009 - 08:55:40 CST)
  - Re: [AMBER] precision in the trajectory files Jenny Iskrenova (Tue Feb 03 2009 - 11:07:58 CST)
[AMBER] Radius of Gyration Beale, John (Mon Feb 02 2009 - 11:34:35 CST)
- Re: [AMBER] Radius of Gyration priya priya (Tue Feb 03 2009 - 23:30:07 CST)
[AMBER] Langevin dynamics Antonios Samiotakis (Mon Feb 02 2009 - 11:54:31 CST)
- Re: [AMBER] Langevin dynamics David A. Case (Mon Feb 02 2009 - 13:24:59 CST)
[AMBER] DFT SK parameter for P atom Qizhi Cui (Mon Feb 02 2009 - 13:59:19 CST)
- Re: [AMBER] DFT SK parameter for P atom Adrian Roitberg (Mon Feb 02 2009 - 14:24:00 CST)
  - Re: [AMBER] DFT SK parameter for P atom Qizhi Cui (Mon Feb 02 2009 - 15:37:41 CST)
[AMBER] Micelles set-up?? Alexander Schierholt (Tue Feb 03 2009 - 04:09:52 CST)
[AMBER] creating a restart file from md.out oguz gurbulak (Tue Feb 03 2009 - 04:44:10 CST)
- Re: [AMBER] creating a restart file from md.out Carlos Simmerling (Tue Feb 03 2009 - 05:30:44 CST)
  - Re: [AMBER] creating a restart file from md.out oguz gurbulak (Tue Feb 03 2009 - 07:22:45 CST)
[AMBER] nab compile error with -scalapack chaitanya koppisetty (Tue Feb 03 2009 - 07:23:46 CST)
- Re: [AMBER] nab compile error with -scalapack David A. Case (Tue Feb 03 2009 - 08:27:24 CST)
  - Re: [AMBER] nab compile error with -scalapack chaitanya koppisetty (Tue Feb 03 2009 - 12:52:54 CST)
[AMBER] -MMTSB instalation flag ? Marek Malý (Tue Feb 03 2009 - 09:31:38 CST)
- Re: [AMBER] -MMTSB instalation flag ? Scott Brozell (Tue Feb 03 2009 - 11:06:47 CST)
  - Re: [AMBER] -MMTSB instalation flag ? Marek Malý (Tue Feb 03 2009 - 11:15:04 CST)
    - Re: [AMBER] -MMTSB instalation flag ? Scott Brozell (Tue Feb 03 2009 - 11:38:11 CST)
[AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun drugdesign (Tue Feb 03 2009 - 11:03:20 CST)
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Ye MEI (Tue Feb 03 2009 - 11:12:54 CST)
  - RE: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Ross Walker (Tue Feb 03 2009 - 11:21:07 CST)
    - Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Carlos Simmerling (Tue Feb 03 2009 - 11:39:58 CST)
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Carlos Simmerling (Tue Feb 03 2009 - 11:17:53 CST)
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun drugdesign (Tue Feb 03 2009 - 23:46:19 CST)
  - Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Carlos Simmerling (Wed Feb 04 2009 - 05:16:34 CST)
[AMBER] out error . .. (Tue Feb 03 2009 - 12:58:46 CST)
- Re: [AMBER] out error Carlos Simmerling (Tue Feb 03 2009 - 13:18:39 CST)
[AMBER] MKL error ? Marek Malý (Tue Feb 03 2009 - 17:00:03 CST)
- RE: [AMBER] MKL error ? Ross Walker (Tue Feb 03 2009 - 23:22:48 CST)
  - Re: [AMBER] MKL error ? Marek Malý (Thu Feb 05 2009 - 06:26:05 CST)
    - RE: [AMBER] MKL error ? Ross Walker (Thu Feb 05 2009 - 12:29:45 CST)
    - Re: [AMBER] MKL error ? Marek Malý (Thu Feb 05 2009 - 14:00:10 CST)
[AMBER] a question about umbrella sampling (US) xiaoqin huang (Wed Feb 04 2009 - 11:12:02 CST)
- Re: [AMBER] a question about umbrella sampling (US) Carlos Simmerling (Wed Feb 04 2009 - 11:20:46 CST)
  - RE: [AMBER] a question about umbrella sampling (US) xiaoqin huang (Wed Feb 04 2009 - 16:23:12 CST)
[AMBER] PDB of a specific frame Jason A. Ford-Green (Wed Feb 04 2009 - 13:46:52 CST)
- Re: [AMBER] PDB of a specific frame Carlos Simmerling (Wed Feb 04 2009 - 13:52:49 CST)
[AMBER] compiling errors Gard Nelson (Wed Feb 04 2009 - 18:30:22 CST)
- Re: [AMBER] compiling errors Carlos Simmerling (Wed Feb 04 2009 - 18:35:28 CST)
- RE: [AMBER] compiling errors Ross Walker (Wed Feb 04 2009 - 18:48:14 CST)
[AMBER] Restarting an MD Simulation Hopkins, Robert (Wed Feb 04 2009 - 18:34:16 CST)
- RE: [AMBER] Restarting an MD Simulation Ross Walker (Wed Feb 04 2009 - 21:03:36 CST)
  - RE: [AMBER] Restarting an MD Simulation Ross Walker (Wed Feb 04 2009 - 21:24:56 CST)
[AMBER] pmemd installation in intelmpi Vijay Manickam Achari (Wed Feb 04 2009 - 21:16:06 CST)
- Re: [AMBER] pmemd installation in intelmpi Robert Duke (Wed Feb 04 2009 - 22:34:37 CST)
  - Re: [AMBER] pmemd installation in intelmpi Vijay Manickam Achari (Thu Feb 05 2009 - 02:38:38 CST)
[AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari (Wed Feb 04 2009 - 21:21:14 CST)
- RE: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross (Wed Feb 11 2009 - 13:04:53 CST)
  - RE: [AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari (Thu Feb 12 2009 - 03:12:29 CST)
    - Re: [AMBER] Compiling Carnal Amber7 in Amber9 David A. Case (Thu Feb 12 2009 - 06:58:03 CST)
    - RE: [AMBER] Compiling Carnal Amber7 in Amber9 Ross Walker (Thu Feb 12 2009 - 08:55:54 CST)
- RE: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross (Thu Feb 12 2009 - 14:32:29 CST)
[AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari (Wed Feb 04 2009 - 22:17:38 CST)
- Re: [AMBER] production run terminates due to (*) symbols in xxx.rst vallespardojl_at_chem.leidenuniv.nl (Thu Feb 05 2009 - 04:28:33 CST)
  - Re: [AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari (Thu Feb 05 2009 - 04:58:26 CST)
- Re: [AMBER] production run terminates due to (*) symbols in xxx.rst Bill Ross (Thu Feb 05 2009 - 11:42:55 CST)
  - Re: [AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari (Thu Feb 05 2009 - 20:50:20 CST)
- RE: [AMBER] production run terminates due to (*) symbols in xxx.rst Ross Walker (Thu Feb 05 2009 - 12:58:41 CST)
[AMBER] how can i deal with large number atoms Wang,Ying (Wed Feb 04 2009 - 23:04:23 CST)
[AMBER] How to build reference coordinate file for targeted MD gmail (Thu Feb 05 2009 - 00:44:22 CST)
- Re: [AMBER] How to build reference coordinate file for targeted MD Carlos Simmerling (Thu Feb 05 2009 - 05:19:12 CST)
  - Re: [AMBER] How to build reference coordinate file for targeted MD xiaonan zhang (Thu Feb 05 2009 - 06:00:38 CST)
  - Re: [AMBER] How to build reference coordinate file for targeted MD gmail (Thu Feb 05 2009 - 23:20:59 CST)
    - RE: [AMBER] How to build reference coordinate file for targeted MD Ross Walker (Fri Feb 06 2009 - 02:14:14 CST)
[AMBER] error in executing sander.MPI in amber9 Vijay Manickam Achari (Thu Feb 05 2009 - 02:37:09 CST)
- Re: [AMBER] error in executing sander.MPI in amber9 Atro Tossavainen (Thu Feb 05 2009 - 05:08:59 CST)
[AMBER] Solvation potential and free energies guardiani_at_fi.infn.it (Thu Feb 05 2009 - 06:27:21 CST)
- Re: [AMBER] Solvation potential and free energies Carlos Simmerling (Thu Feb 05 2009 - 06:33:08 CST)
- Re: [AMBER] Solvation potential and free energies Lorenzo Gontrani (Thu Feb 05 2009 - 06:34:47 CST)
- Re: [AMBER] Solvation potential and free energies David A. Case (Fri Feb 06 2009 - 07:34:25 CST)
[AMBER] parameter files for D-amino acid Vsatheesh Patil (Thu Feb 05 2009 - 07:04:12 CST)
- Re: [AMBER] parameter files for D-amino acid Carlos Simmerling (Thu Feb 05 2009 - 07:37:32 CST)
  - Re: [AMBER] parameter files for D-amino acid vijayaraj_at_clri.res.in (Thu Feb 05 2009 - 08:49:56 CST)
[AMBER] pmemd on BlueGene/P? Hannes Loeffler (Thu Feb 05 2009 - 07:09:45 CST)
- Re: [AMBER] pmemd on BlueGene/P? Robert Duke (Thu Feb 05 2009 - 07:42:32 CST)
- Re: [AMBER] pmemd on BlueGene/P? Carlos P Sosa (Thu Feb 05 2009 - 14:48:57 CST)
  - Re: [AMBER] pmemd on BlueGene/P? Hannes Loeffler (Fri Feb 06 2009 - 03:01:37 CST)
Re: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross (Thu Feb 05 2009 - 11:36:00 CST)
- Re: [AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari (Wed Feb 11 2009 - 01:58:08 CST)
  - RE: [AMBER] Compiling Carnal Amber7 in Amber9 Ross Walker (Wed Feb 11 2009 - 10:53:10 CST)
[AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari (Fri Feb 06 2009 - 01:00:16 CST)
- Re: [AMBER] amber9 installation problem in SMP IA64 David A. Case (Fri Feb 06 2009 - 07:25:55 CST)
  - Re: [AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari (Tue Feb 10 2009 - 02:30:55 CST)
[AMBER] mpirun problem in HPC Vijay Manickam Achari (Fri Feb 06 2009 - 01:01:29 CST)
- RE: [AMBER] mpirun problem in HPC Ross Walker (Fri Feb 06 2009 - 02:05:37 CST)
[AMBER] second derivative matrix calculation Marie Brut (Fri Feb 06 2009 - 04:47:18 CST)
- Re: [AMBER] second derivative matrix calculation David A. Case (Fri Feb 06 2009 - 07:19:52 CST)
[AMBER] extract frames from a .mdcrd vallespardojl_at_chem.leidenuniv.nl (Fri Feb 06 2009 - 04:48:23 CST)
- Re: [AMBER] extract frames from a .mdcrd Carlos Simmerling (Fri Feb 06 2009 - 05:12:00 CST)
  - Re: [AMBER] extract frames from a .mdcrd vallespardojl_at_chem.leidenuniv.nl (Tue Feb 10 2009 - 02:52:19 CST)
    - Re: [AMBER] extract frames from a .mdcrd Carlos Simmerling (Tue Feb 10 2009 - 04:58:12 CST)
- Re: [AMBER] extract frames from a .mdcrd Bill Ross (Fri Feb 06 2009 - 13:13:27 CST)
[AMBER] MSD and stress tensors oguz gurbulak (Fri Feb 06 2009 - 05:09:12 CST)
[AMBER] script to convert GLYCAM ff in CHARMM format ABEL Stephane 175950 (Fri Feb 06 2009 - 08:39:04 CST)
- Re: [AMBER] script to convert GLYCAM ff in CHARMM format Lachele Foley (Lists) (Fri Feb 06 2009 - 08:57:17 CST)
  - RE : [AMBER] script to convert GLYCAM ff in CHARMM format ABEL Stephane 175950 (Fri Feb 06 2009 - 09:03:19 CST)
[AMBER] Resp charge . .. (Fri Feb 06 2009 - 11:34:12 CST)
- Re: [AMBER] Resp charge Jason A. Ford-Green (Fri Feb 06 2009 - 14:38:29 CST)
[AMBER] ptraj fails to recognize binary REMD output Kevin Wiehe (Fri Feb 06 2009 - 11:44:21 CST)
[AMBER] distance calculation by reading in the restraint file xiaoqin huang (Fri Feb 06 2009 - 11:52:56 CST)
- RE: [AMBER] distance calculation by reading in the restraint file xiaoqin huang (Fri Feb 06 2009 - 12:34:34 CST)
  - Re: [AMBER] distance calculation by reading in the restraint file David A. Case (Fri Feb 06 2009 - 16:35:55 CST)
    - RE: [AMBER] distance calculation by reading in the restraint file xiaoqin huang (Fri Feb 06 2009 - 17:28:59 CST)
- Re: [AMBER] distance calculation by reading in the restraint file David A. Case (Fri Feb 06 2009 - 16:03:08 CST)
[AMBER] MD analysis oguz gurbulak (Sat Feb 07 2009 - 08:56:10 CST)
[AMBER] Stability of a long NPT md trajectory? Bill K (Mon Feb 09 2009 - 01:07:24 CST)
- Re: [AMBER] Stability of a long NPT md trajectory? Carlos Simmerling (Mon Feb 09 2009 - 06:08:29 CST)
  - Re: [AMBER] Stability of a long NPT md trajectory? Robert Duke (Mon Feb 09 2009 - 07:25:10 CST)
[AMBER] second derivative matrix Marie Brut (Mon Feb 09 2009 - 02:53:01 CST)
- Re: [AMBER] second derivative matrix Adrian Roitberg (Mon Feb 09 2009 - 08:29:51 CST)
- Re: [AMBER] second derivative matrix David A. Case (Mon Feb 09 2009 - 09:05:18 CST)
[AMBER] NAB md function prints strange output Jochen Heil (Mon Feb 09 2009 - 05:30:21 CST)
- Re: [AMBER] NAB md function prints strange output David A. Case (Mon Feb 09 2009 - 06:58:43 CST)
  - Re: [AMBER] NAB md function prints strange output Jochen Heil (Tue Feb 10 2009 - 06:19:56 CST)
    - Re: [AMBER] NAB md function prints strange output David A. Case (Tue Feb 10 2009 - 06:46:40 CST)
    - Re: [AMBER] NAB md function prints strange output Scott Brozell (Thu Mar 12 2009 - 16:04:15 CDT)
[AMBER] APS & ff03 Mahmoud A. A. Ibrahim (Mon Feb 09 2009 - 08:49:56 CST)
[AMBER] parmchk s. Bill (Mon Feb 09 2009 - 09:55:20 CST)
- RE: [AMBER] parmchk Ross Walker (Mon Feb 09 2009 - 10:28:20 CST)
[AMBER] hbond analysis aneesh cna (Mon Feb 09 2009 - 11:55:25 CST)
- Re: [AMBER] hbond analysis Bala subramanian (Mon Feb 09 2009 - 12:33:39 CST)
- Re: [AMBER] hbond analysis Carlos Simmerling (Mon Feb 09 2009 - 12:52:14 CST)
[AMBER] Solvating inside of a channel Daniel Smith (Mon Feb 09 2009 - 15:03:16 CST)
[AMBER] Confusion regarding box size parul sharma (Tue Feb 10 2009 - 01:20:01 CST)
- Re: [AMBER] Confusion regarding box size vallespardojl_at_chem.leidenuniv.nl (Tue Feb 10 2009 - 02:35:24 CST)
- Re: [AMBER] Confusion regarding box size Wei Zhang (Tue Feb 10 2009 - 07:07:38 CST)
  - Re: [AMBER] Confusion regarding box size parul sharma (Tue Feb 10 2009 - 07:29:38 CST)
[AMBER] Irregularity in box during md parul sharma (Tue Feb 10 2009 - 04:35:18 CST)
- Re: [AMBER] Irregularity in box during md Carlos Simmerling (Tue Feb 10 2009 - 04:57:02 CST)
- Re: [AMBER] Irregularity in box during md Bill Ross (Tue Feb 10 2009 - 11:24:12 CST)
[AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] Patrick Schopf (Tue Feb 10 2009 - 08:15:42 CST)
- RE : [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] ABEL Stephane 175950 (Tue Feb 10 2009 - 08:39:17 CST)
- Re: [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] FyD (Tue Feb 10 2009 - 09:05:56 CST)
[AMBER] Scaling of dipole interactions Diddo Diddens (Tue Feb 10 2009 - 08:33:18 CST)
[AMBER] formate parameters Dmitri Nilov (Tue Feb 10 2009 - 08:47:31 CST)
[AMBER] array out of bound in Amber10 tests Shan-ho Tsai (Tue Feb 10 2009 - 10:19:42 CST)
- Re: [AMBER] array out of bound in Amber10 tests David A. Case (Tue Feb 10 2009 - 10:39:43 CST)
  - Re: [AMBER] array out of bound in Amber10 tests Shan-ho Tsai (Tue Feb 10 2009 - 15:04:43 CST)
[AMBER] reg . run TMD balaji nagarajan (Tue Feb 10 2009 - 11:36:28 CST)
- Re: [AMBER] reg . run TMD Carlos Simmerling (Tue Feb 10 2009 - 11:48:22 CST)
[AMBER] Solvating the interior of a channel Daniel Smith (Tue Feb 10 2009 - 14:42:09 CST)
- Re: [AMBER] Solvating the interior of a channel Shozeb Haider (Wed Feb 11 2009 - 07:15:07 CST)
- Re: [AMBER] Solvating the interior of a channel Jason A. Ford-Green (Wed Feb 11 2009 - 10:04:24 CST)
  - Re: [AMBER] Solvating the interior of a channel Daniel Smith (Fri Feb 13 2009 - 15:02:24 CST)
    - Re: [AMBER] Solvating the interior of a channel Daniel Smith (Sun Feb 15 2009 - 16:40:23 CST)
[AMBER] AMBER: chiral restraint on protein amit jain (Tue Feb 10 2009 - 18:48:12 CST)
- Re: [AMBER] AMBER: chiral restraint on protein David A. Case (Wed Feb 11 2009 - 06:56:05 CST)
[AMBER] how to get amber 10 Prem Prakash Pathak (Tue Feb 10 2009 - 20:42:37 CST)
- RE: [AMBER] how to get amber 10 Ross Walker (Tue Feb 10 2009 - 21:20:33 CST)
[AMBER] nmr refinement of dimer Sally Pias (Wed Feb 11 2009 - 03:05:56 CST)
- Re: [AMBER] nmr refinement of dimer Therese Malliavin (Wed Feb 11 2009 - 04:57:06 CST)
- Re: [AMBER] nmr refinement of dimer David A. Case (Wed Feb 11 2009 - 07:02:37 CST)
  - Re: [AMBER] nmr refinement of dimer Sally Pias (Thu Feb 12 2009 - 03:17:44 CST)
    - Re: [AMBER] nmr refinement of dimer David A. Case (Thu Feb 12 2009 - 07:08:08 CST)
[AMBER] lmod calculation for complexe . .. (Wed Feb 11 2009 - 03:09:04 CST)
[AMBER] Optimization problem Daniel Emery (Thu Feb 12 2009 - 04:01:49 CST)
- Re: [AMBER] Optimization problem David A. Case (Thu Feb 12 2009 - 06:58:17 CST)
  - Re: [AMBER] Optimization problem Daniel Emery (Thu Feb 12 2009 - 08:11:14 CST)
- Re: [AMBER] Optimization problem Gustavo Seabra (Thu Feb 12 2009 - 08:48:23 CST)
[AMBER] error in xleap: ligand binding using MMand QMMM tech kureeckal ramesh (Thu Feb 12 2009 - 04:27:41 CST)
- Re: [AMBER] error in xleap: ligand binding using MMand QMMM tech Gustavo Seabra (Thu Feb 12 2009 - 08:32:17 CST)
[AMBER] H-bond information Beale, John (Thu Feb 12 2009 - 09:32:30 CST)
[AMBER] projections of trajectories onto the first 2 principal eigenvectors Carra, Claudio (JSC-SK)[USRA] (Thu Feb 12 2009 - 12:22:20 CST)
- Re: [AMBER] projections of trajectories onto the first 2 principal eigenvectors Hannes Loeffler (Fri Feb 13 2009 - 02:32:20 CST)
  - Re: [AMBER] projections of trajectories onto the first 2 principal eigenvectors Hannes Loeffler (Fri Feb 13 2009 - 03:33:19 CST)
[AMBER] atoms fly out of the box in NVT calculations iccy liu (Thu Feb 12 2009 - 15:48:24 CST)
- Re: [AMBER] atoms fly out of the box in NVT calculations Carlos Simmerling (Thu Feb 12 2009 - 16:05:10 CST)
- Re: [AMBER] atoms fly out of the box in NVT calculations Ross Walker (Thu Feb 12 2009 - 20:22:57 CST)
  - RE: [AMBER] atoms fly out of the box in NVT calculations iccy liu (Sun Feb 15 2009 - 17:34:37 CST)
[AMBER] How to jude whether the trajectory is stable or not Jeffrey (Thu Feb 12 2009 - 20:33:53 CST)
[AMBER] Beginner question Heath Watts (Fri Feb 13 2009 - 15:18:42 CST)
- Re: [AMBER] Beginner question Carlos Simmerling (Fri Feb 13 2009 - 15:24:37 CST)
  - Re: [AMBER] Beginner question Heath Watts (Fri Feb 13 2009 - 19:19:44 CST)
- Re: [AMBER] Beginner question Barbault Florent (Fri Feb 13 2009 - 15:25:13 CST)
  - Re: [AMBER] Beginner question Heath Watts (Fri Feb 13 2009 - 19:20:46 CST)
[AMBER] Question about improper torsions... Antonios Samiotakis (Fri Feb 13 2009 - 16:57:03 CST)
- Re: [AMBER] Question about improper torsions... David A. Case (Sat Feb 14 2009 - 07:32:21 CST)
[AMBER] New atom type with 7 bonds Akansha Saxena (Fri Feb 13 2009 - 17:56:47 CST)
- Re: [AMBER] New atom type with 7 bonds David A. Case (Mon Feb 16 2009 - 08:28:25 CST)
[AMBER] install Amber 10 to Macbook Adrien Delmont (Sat Feb 14 2009 - 05:06:50 CST)
- Re: [AMBER] install Amber 10 to Macbook David A. Case (Sat Feb 14 2009 - 17:17:53 CST)
  - Re: [AMBER] install Amber 10 to Macbook Tyler Luchko (Sun Feb 15 2009 - 13:27:53 CST)
    - Re: [AMBER] install Amber 10 to Macbook David Watson (Sun Feb 15 2009 - 13:52:36 CST)
[AMBER] Any link to a major QM code? Francesco Pietra (Sun Feb 15 2009 - 11:58:30 CST)
- Re: [AMBER] Any link to a major QM code? Gustavo Seabra (Sun Feb 15 2009 - 18:17:32 CST)
  - Re: [AMBER] Any link to a major QM code? Adrian Roitberg (Sun Feb 15 2009 - 20:59:01 CST)
    - Re: [AMBER] Any link to a major QM code? Francesco Pietra (Mon Feb 16 2009 - 08:47:04 CST)
    - Re: [AMBER] Any link to a major QM code? Gustavo Seabra (Mon Feb 16 2009 - 10:51:03 CST)
[AMBER] Error running sander.MPI Vijay Manickam Achari (Mon Feb 16 2009 - 02:23:05 CST)
- Re: [AMBER] Error running sander.MPI Carlos Simmerling (Mon Feb 16 2009 - 05:51:08 CST)
- RE: [AMBER] Error running sander.MPI Rausch, Felix (Tue Feb 17 2009 - 02:15:19 CST)
  - Re: [AMBER] Error running sander.MPI Anselm Horn (Tue Feb 17 2009 - 04:28:47 CST)
[AMBER] Error installing Amber David Patiño (Mon Feb 16 2009 - 06:02:31 CST)
- Re: [AMBER] Error installing Amber David A. Case (Mon Feb 16 2009 - 08:21:41 CST)
  - Re: [AMBER] Error installing Amber David Patiño (Tue Feb 17 2009 - 08:58:05 CST)
[AMBER] Iron 2+ parameters Hrvoje Brkiæ (Mon Feb 16 2009 - 07:53:57 CST)
- Re: [AMBER] Iron 2+ parameters Syed Tarique Moin (Mon Feb 16 2009 - 10:25:34 CST)
- Re: [AMBER] Iron 2+ parameters FyD (Mon Feb 16 2009 - 12:25:45 CST)
[AMBER] density and volume in NVT ensamble oguz gurbulak (Mon Feb 16 2009 - 07:58:13 CST)
- Re: [AMBER] density and volume in NVT ensamble Carlos Simmerling (Mon Feb 16 2009 - 08:04:22 CST)
  - Re: [AMBER] density and volume in NVT ensamble oguz gurbulak (Mon Feb 16 2009 - 08:25:52 CST)
- Re: [AMBER] density and volume in NVT ensamble Andrew Purkiss-Trew (Mon Feb 16 2009 - 08:14:40 CST)
  - Re: [AMBER] density and volume in NVT ensamble oguz gurbulak (Mon Feb 16 2009 - 08:32:07 CST)
    - Re: [AMBER] density and volume in NVT ensamble Andrew Purkiss-Trew (Mon Feb 16 2009 - 08:45:25 CST)
[AMBER] contant force pulling simulation with amber 10 li hui (Mon Feb 16 2009 - 11:01:36 CST)
- Re: [AMBER] contant force pulling simulation with amber 10 Gustavo Seabra (Mon Feb 16 2009 - 12:11:40 CST)
[AMBER] can ptraj output the trajectory of the residue CM? Jose Borreguero (Mon Feb 16 2009 - 13:47:34 CST)
[AMBER] using ptraj Molecular Dynamics (Mon Feb 16 2009 - 14:31:42 CST)
- Re: [AMBER] using ptraj Carlos Simmerling (Mon Feb 16 2009 - 14:41:54 CST)
  - Re: [AMBER] using ptraj Molecular Dynamics (Tue Feb 17 2009 - 05:44:09 CST)
[AMBER] Normal errors on job kill? ben rodriguez (Mon Feb 16 2009 - 20:35:43 CST)
- Re: [AMBER] Normal errors on job kill? David A. Case (Mon Feb 16 2009 - 22:25:54 CST)
[AMBER] Amber 9 Install - AMBERBUILDFLAGS error ben rodriguez (Mon Feb 16 2009 - 21:39:14 CST)
- Re: [AMBER] Amber 9 Install - AMBERBUILDFLAGS error David A. Case (Mon Feb 16 2009 - 22:29:41 CST)
[AMBER] parallel run error balaji nagarajan (Tue Feb 17 2009 - 02:19:23 CST)
- Re: [AMBER] parallel run error Carlos Simmerling (Tue Feb 17 2009 - 06:40:03 CST)
[AMBER] constph tutorial help Prem Prakash Pathak (Tue Feb 17 2009 - 06:53:37 CST)
[AMBER] (no subject) Beale, John (Tue Feb 17 2009 - 07:02:25 CST)
- Re: [AMBER] (no subject) Carlos Simmerling (Tue Feb 17 2009 - 07:10:49 CST)
[AMBER] MD simulation with a partially flexible system Jeffrey (Tue Feb 17 2009 - 08:38:10 CST)
- Re: [AMBER] MD simulation with a partially flexible system Carlos Simmerling (Tue Feb 17 2009 - 08:45:33 CST)
  - Re: Re: [AMBER] MD simulation with a partially flexible system Jeffrey (Tue Feb 17 2009 - 20:19:47 CST)
    - Re: Re: [AMBER] MD simulation with a partially flexible system Carlos Simmerling (Wed Feb 18 2009 - 06:35:40 CST)
[AMBER] DM complexation . .. (Tue Feb 17 2009 - 09:10:49 CST)
- Re: [AMBER] DM complexation Carlos Simmerling (Tue Feb 17 2009 - 09:28:34 CST)
  - RE: [AMBER] DM complexation . .. (Tue Feb 17 2009 - 09:36:01 CST)
    - Re: [AMBER] DM complexation Carlos Simmerling (Tue Feb 17 2009 - 09:59:15 CST)
[AMBER] How to get the energy of a molecule in a whole system Wang,Ying (Tue Feb 17 2009 - 10:28:39 CST)
[AMBER] restraint angle m m (Tue Feb 17 2009 - 11:17:00 CST)
- Re: [AMBER] restraint angle David A. Case (Tue Feb 17 2009 - 11:52:49 CST)
[AMBER] PMF calculation Arnaud (Tue Feb 17 2009 - 12:10:18 CST)
- Re: [AMBER] PMF calculation David A. Case (Tue Feb 17 2009 - 20:23:20 CST)
[AMBER] Need suggestion on payment for Ph.D student majored in molecular simulation Xu Dong (Tue Feb 17 2009 - 12:54:58 CST)
- Re: [AMBER] Need suggestion on payment for Ph.D student majored in molecular simulation Adrian Roitberg (Tue Feb 17 2009 - 12:57:56 CST)
[AMBER] glycam and solvateoct command Heath Watts (Tue Feb 17 2009 - 13:51:13 CST)
- Re: [AMBER] glycam and solvateoct command Barbault Florent (Tue Feb 17 2009 - 14:13:58 CST)
  - Re: [AMBER] glycam and solvateoct command Heath Watts (Tue Feb 17 2009 - 16:31:35 CST)
    - Re: [AMBER] glycam and solvateoct command Lachele Foley (Lists) (Wed Feb 18 2009 - 09:00:34 CST)
[AMBER] problem compiling nmode.c Shan-ho Tsai (Tue Feb 17 2009 - 14:38:00 CST)
- Re: [AMBER] problem compiling nmode.c David A. Case (Tue Feb 17 2009 - 20:45:03 CST)
  - [AMBER] NVT vs NPT Chih-Ying Lin (Tue Feb 17 2009 - 21:23:05 CST)
  - Re: [AMBER] problem compiling nmode.c Shan-ho Tsai (Thu Feb 19 2009 - 08:49:39 CST)
[AMBER] reg.Targeted molecular dynamics balaji nagarajan (Tue Feb 17 2009 - 23:26:49 CST)
- Re: [AMBER] reg.Targeted molecular dynamics Simon Becker (Wed Feb 18 2009 - 05:38:54 CST)
  - RE: [AMBER] reg.Targeted molecular dynamics balaji nagarajan (Wed Feb 18 2009 - 08:07:09 CST)
[AMBER] protein monomerizartion times and simulation with implicit solvent drugdesign (Wed Feb 18 2009 - 04:27:17 CST)
- Re: [AMBER] protein monomerizartion times and simulation with implicit solvent Carlos Simmerling (Wed Feb 18 2009 - 06:16:00 CST)
[AMBER] Re: AMBER: GBSA EGB = NaN Markus Kaukonen (Wed Feb 18 2009 - 06:26:28 CST)
- [AMBER] Re: AMBER: GBSA EGB = NaN Markus Kaukonen (Thu Feb 19 2009 - 07:34:38 CST)
[AMBER] IG not change at each restart of NPT simulation Jeffrey (Wed Feb 18 2009 - 06:49:47 CST)
- Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke (Wed Feb 18 2009 - 07:57:35 CST)
  - Re: [AMBER] IG not change at each restart of NPT simulation Carlos Simmerling (Wed Feb 18 2009 - 08:04:47 CST)
    - Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke (Wed Feb 18 2009 - 08:15:00 CST)
    - Re: [AMBER] IG not change at each restart of NPT simulation Adrian Roitberg (Wed Feb 18 2009 - 08:46:36 CST)
- Re: [AMBER] IG not change at each restart of NPT simulation Hopkins, Robert (Wed Mar 18 2009 - 17:55:33 CDT)
  - RE: [AMBER] IG not change at each restart of NPT simulation Ross Walker (Wed Mar 18 2009 - 18:07:07 CDT)
[AMBER] How to constrain the hydrogen bonding distances... Majeed Shaik (Wed Feb 18 2009 - 08:11:37 CST)
- Re: [AMBER] How to constrain the hydrogen bonding distances... Carlos Simmerling (Wed Feb 18 2009 - 08:25:47 CST)
- Re: [AMBER] How to constrain the hydrogen bonding distances... David A. Case (Wed Feb 18 2009 - 08:28:56 CST)
[AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory Andrew Olson (Wed Feb 18 2009 - 11:08:57 CST)
- Re: [AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory David A. Case (Wed Feb 18 2009 - 12:11:56 CST)
[AMBER] question about ptraj hydrogen bond analysis monica bhattacharee (Wed Feb 18 2009 - 13:45:17 CST)
- Re: [AMBER] question about ptraj hydrogen bond analysis Thomas Cheatham III (Wed Feb 18 2009 - 14:21:27 CST)
[AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error Majeed Shaik (Wed Feb 18 2009 - 14:09:17 CST)
- Re: [AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error David A. Case (Wed Feb 18 2009 - 14:35:12 CST)
[AMBER] Re: AMBER: How do you evaluate forces on a fixed atom? Bill Kowallis (Wed Feb 18 2009 - 19:55:47 CST)
[AMBER] test charge Dan Kaps (Wed Feb 18 2009 - 20:27:32 CST)
- Re: [AMBER] test charge David A. Case (Wed Feb 18 2009 - 22:24:04 CST)
  - Re: [AMBER] test charge Dan Kaps (Thu Feb 19 2009 - 20:22:31 CST)
[AMBER] distance matrix plot and secondary structure analysis Siddharth Rastogi (Thu Feb 19 2009 - 00:17:47 CST)
- Re: [AMBER] distance matrix plot and secondary structure analysis Carlos Simmerling (Thu Feb 19 2009 - 06:48:57 CST)
[AMBER] Protein motions comparison Dmitry Osolodkin (Thu Feb 19 2009 - 05:58:24 CST)
- Re: [AMBER] Protein motions comparison Hannes Loeffler (Thu Feb 19 2009 - 06:07:47 CST)
[AMBER] secstruct Beale, John (Thu Feb 19 2009 - 07:22:20 CST)
- Re: [AMBER] secstruct Carlos Simmerling (Thu Feb 19 2009 - 07:30:16 CST)
[AMBER] dipole correlation function Jeffrey (Thu Feb 19 2009 - 08:18:20 CST)
- Re: [AMBER] dipole correlation function Carlos Simmerling (Thu Feb 19 2009 - 08:39:16 CST)
  - Re: Re: [AMBER] dipole correlation function Jeffrey (Thu Feb 19 2009 - 10:39:15 CST)
[AMBER] paper of interest for FF development/solvent models David Mobley (Thu Feb 19 2009 - 09:15:04 CST)
[AMBER] (no subject) Andrew Olson (Thu Feb 19 2009 - 13:46:24 CST)
[AMBER] Antechamber kureeckal ramesh (Thu Feb 19 2009 - 19:36:03 CST)
[AMBER] Problem with NVT and NPT parul sharma (Fri Feb 20 2009 - 07:07:36 CST)
- Re: [AMBER] Problem with NVT and NPT Adrian Roitberg (Fri Feb 20 2009 - 07:14:23 CST)
  - Re: [AMBER] Problem with NVT and NPT parul sharma (Fri Feb 20 2009 - 07:27:51 CST)
    - Re: [AMBER] Problem with NVT and NPT Carlos Simmerling (Fri Feb 20 2009 - 07:30:26 CST)
[AMBER] Parmchk wrongly calculates missing parameters (fwd) Gijs Schaftenaar (Fri Feb 20 2009 - 07:16:17 CST)
[AMBER] ACS computational chemistry awards - March 9th deadline Carlos Simmerling (Fri Feb 20 2009 - 10:27:18 CST)
[AMBER] order of "upper" and "lower" bounds in the makeDIS_RST inputs Piotr Cieplak (Fri Feb 20 2009 - 15:40:14 CST)
- Re: [AMBER] order of "upper" and "lower" bounds in the makeDIS_RST inputs David A. Case (Sat Feb 21 2009 - 17:51:38 CST)
[AMBER] reg.targeted molecular dynamics balaji nagarajan (Fri Feb 20 2009 - 23:10:50 CST)
- Re: [AMBER] reg.targeted molecular dynamics Carlos Simmerling (Sat Feb 21 2009 - 06:35:05 CST)
  - RE: [AMBER] reg.targeted molecular dynamics balaji nagarajan (Sun Feb 22 2009 - 08:45:29 CST)
[AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Xu Dong (Sat Feb 21 2009 - 14:27:29 CST)
- Re: [AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Carlos Simmerling (Sat Feb 21 2009 - 15:33:31 CST)
  - Re: [AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Xu Dong (Sat Feb 21 2009 - 15:40:03 CST)
[AMBER] PME doesn't work parul sharma (Mon Feb 23 2009 - 03:43:40 CST)
- Re: [AMBER] PME doesn't work Carlos Simmerling (Mon Feb 23 2009 - 05:19:27 CST)
  - Re: [AMBER] PME doesn't work parul sharma (Mon Feb 23 2009 - 06:03:54 CST)
    - Re: [AMBER] PME doesn't work Carlos Simmerling (Mon Feb 23 2009 - 06:08:07 CST)
- Re: [AMBER] PME doesn't work Robert Duke (Mon Feb 23 2009 - 07:48:04 CST)
[AMBER] PMEMD vs GROMACS? Sasha Buzko (Mon Feb 23 2009 - 13:55:27 CST)
- Re: [AMBER] PMEMD vs GROMACS? Vlad Cojocaru (Tue Feb 24 2009 - 02:24:16 CST)
  - Re: [AMBER] PMEMD vs GROMACS? Hannes Loeffler (Tue Feb 24 2009 - 02:39:29 CST)
    - Re: [AMBER] PMEMD vs GROMACS? Vlad Cojocaru (Tue Feb 24 2009 - 02:46:36 CST)
  - Re: [AMBER] PMEMD vs GROMACS? Sasha Buzko (Tue Feb 24 2009 - 11:15:59 CST)
[AMBER] problem with amber installation nicholus bhattacharjee (Tue Feb 24 2009 - 00:50:12 CST)
- Re: [AMBER] problem with amber installation Carlos Simmerling (Tue Feb 24 2009 - 05:47:20 CST)
  - Re: [AMBER] problem with amber installation nicholus bhattacharjee (Tue Feb 24 2009 - 22:29:11 CST)
[AMBER] follow-up to previous discussion: nmr refinement of dimer Sally Pias (Tue Feb 24 2009 - 01:50:41 CST)
- Re: [AMBER] follow-up to previous discussion: nmr refinement of dimer David A. Case (Tue Feb 24 2009 - 07:15:27 CST)
[AMBER] About the croase grainded FF James W (Tue Feb 24 2009 - 01:58:12 CST)
- Re: [AMBER] About the croase grainded FF Vlad Cojocaru (Tue Feb 24 2009 - 02:40:53 CST)
[AMBER] (no subject) Beale, John (Tue Feb 24 2009 - 05:59:51 CST)
[AMBER] amber tools reading netcdf files Jeremy Harris (Tue Feb 24 2009 - 09:54:09 CST)
- Re: [AMBER] amber tools reading netcdf files Chris Moth (Tue Feb 24 2009 - 11:35:22 CST)
  - RE: [AMBER] amber tools reading netcdf files Cojocaru,Vlad (Tue Feb 24 2009 - 12:46:27 CST)
[AMBER] perform an analysis using ptraj oguz gurbulak (Tue Feb 24 2009 - 10:19:11 CST)
[AMBER] Equilibration Scaling to System Size Hopkins, Robert (Tue Feb 24 2009 - 16:31:37 CST)
- Re: [AMBER] Equilibration Scaling to System Size Carlos Simmerling (Tue Feb 24 2009 - 16:49:10 CST)
[AMBER] problem about trajectory analysis Adrien Delmont (Wed Feb 25 2009 - 08:24:41 CST)
- Re: [AMBER] problem about trajectory analysis Thomas Cheatham III (Wed Feb 25 2009 - 18:57:49 CST)
[AMBER] (no subject) waleed zalloum (Wed Feb 25 2009 - 10:41:14 CST)
- Re: [AMBER] (no subject) Thomas Cheatham III (Wed Feb 25 2009 - 18:48:56 CST)
[AMBER] ptraj analyze Beale, John (Wed Feb 25 2009 - 10:56:59 CST)
- Re: [AMBER] ptraj analyze Thomas Cheatham III (Wed Feb 25 2009 - 18:45:17 CST)
[AMBER] Simulated annealing Ibrahim Moustafa (Wed Feb 25 2009 - 18:26:37 CST)
- Re: [AMBER] Simulated annealing Carlos Simmerling (Wed Feb 25 2009 - 19:31:30 CST)
  - Re: [AMBER] Simulated annealing Ibrahim Moustafa (Thu Feb 26 2009 - 09:28:44 CST)
[AMBER] Error in using Amber sri noraima othman (Wed Feb 25 2009 - 21:27:29 CST)
- RE: [AMBER] Error in using Amber Ross Walker (Thu Feb 26 2009 - 00:03:12 CST)
  - Re: [AMBER] Error in using Amber sri noraima othman (Thu Feb 26 2009 - 00:27:14 CST)
[AMBER] tleap errors !! Sampath Koppole (Thu Feb 26 2009 - 03:47:48 CST)
- Re: [AMBER] tleap errors !! David A. Case (Thu Feb 26 2009 - 07:45:49 CST)
[AMBER] MD simulation at constant pH Francesco Pietra (Thu Feb 26 2009 - 04:52:47 CST)
[AMBER] Current Amber10 bugfix.all doesn't apply cleanly Mark Dixon (Thu Feb 26 2009 - 05:54:03 CST)
- Re: [AMBER] Current Amber10 bugfix.all doesn't apply cleanly Mark Dixon (Fri Feb 27 2009 - 10:44:28 CST)
[AMBER] PLUMED release 1.0.0 available Massimiliano Bonomi (Thu Feb 26 2009 - 07:11:54 CST)
[AMBER] extra torsion terms in tleap.top-file Astrid Maaß (Thu Feb 26 2009 - 08:32:30 CST)
[AMBER] H-Bonds Beale, John (Thu Feb 26 2009 - 08:38:04 CST)
- Re: [AMBER] H-Bonds Thomas Cheatham III (Wed Mar 04 2009 - 15:00:30 CST)
  - [AMBER] What is the default position of the partial charges? Chih-Ying Lin (Wed Mar 04 2009 - 15:06:16 CST)
    - Re: [AMBER] What is the default position of the partial charges? Thomas Cheatham III (Wed Mar 04 2009 - 15:44:20 CST)
  - [AMBER] solvent and counter ions Taufik Al-Sarraj (Wed Mar 04 2009 - 15:36:36 CST)
[AMBER] (no subject) Lake, Thomas (Thu Feb 26 2009 - 10:19:53 CST)
- Re: [AMBER] (no subject) Carlos Simmerling (Thu Feb 26 2009 - 10:24:40 CST)
- [AMBER] MD simulations on a protein with FAD and NADH Mannan (Thu Feb 26 2009 - 19:11:54 CST)
  - RE: [AMBER] MD simulations on a protein with FAD and NADH Ross Walker (Thu Feb 26 2009 - 22:32:05 CST)
  - Re: [AMBER] MD simulations on a protein with FAD and NADH FyD (Fri Feb 27 2009 - 02:24:37 CST)
[AMBER] A problem with xleap and pdb file nancy4619 (Fri Feb 27 2009 - 06:28:01 CST)
- Re: [AMBER] A problem with xleap and pdb file David A. Case (Fri Feb 27 2009 - 07:56:26 CST)
  - Re:Re: [AMBER] A problem with xleap and pdb file nancy4619 (Fri Feb 27 2009 - 08:20:17 CST)
    - Re:Re: [AMBER] A problem with xleap and pdb file Peter Gannett (Fri Feb 27 2009 - 08:32:20 CST)
    - RE: Re: [AMBER] A problem with xleap and pdb file Ross Walker (Fri Feb 27 2009 - 09:55:23 CST)
[AMBER] Re: Antechamber kureeckal ramesh (Fri Feb 27 2009 - 06:56:58 CST)
- Re: [AMBER] Re: Antechamber FyD (Fri Feb 27 2009 - 07:12:16 CST)
  - Re:Re: [AMBER] Re: Antechamber null (Fri Feb 27 2009 - 08:00:07 CST)
[AMBER] I need a professional help about xleap and pdb file nancy4619 (Fri Feb 27 2009 - 07:56:14 CST)
- Re: [AMBER] I need a professional help about xleap and pdb file Peter Gannett (Fri Feb 27 2009 - 08:17:31 CST)
[AMBER] using Gromacs for analysis oguz gurbulak (Fri Feb 27 2009 - 11:03:54 CST)
- Re: [AMBER] using Gromacs for analysis Bala subramanian (Fri Feb 27 2009 - 12:16:46 CST)
- [AMBER] Re: using Gromacs for analysis oguz gurbulak (Mon Mar 02 2009 - 10:17:45 CST)
[AMBER] Partial entropy calculations ? Marek Malý (Fri Feb 27 2009 - 12:21:29 CST)
- Re: [AMBER] Partial entropy calculations ? Piotr Cieplak (Fri Feb 27 2009 - 12:44:21 CST)
[AMBER] PCL waleed zalloum (Sat Feb 28 2009 - 11:17:51 CST)
- RE: [AMBER] PCL Ross Walker (Sat Feb 28 2009 - 11:23:30 CST)
[AMBER] a query Molecular Dynamics (Sat Feb 28 2009 - 13:45:46 CST)
[AMBER] IMPORTANT INFO: Regarding Anonymous postings to the AMBER mailing list. Ross Walker (Sat Feb 28 2009 - 16:19:16 CST)
[AMBER] Question about NAB module Wei Huang (Sat Feb 28 2009 - 18:23:49 CST)
- Re: [AMBER] Question about NAB module David A. Case (Sun Mar 01 2009 - 07:52:19 CST)
  - RE: [AMBER] Question about NAB module Wei Huang (Sun Mar 01 2009 - 08:57:50 CST)
    - RE: [AMBER] Question about NAB module Andreas Svrcek-Seiler (Mon Mar 02 2009 - 03:23:52 CST)
[AMBER] binding free energy Maryam Hamzehee (Sun Mar 01 2009 - 05:52:43 CST)
- Re: [AMBER] binding free energy Barbault Florent (Sun Mar 01 2009 - 06:20:39 CST)
  - Re: [AMBER] binding free energy Don.Bashford_at_stjude.org (Sun Mar 01 2009 - 11:18:39 CST)
[AMBER] Pseudoatoms waleed zalloum (Mon Mar 02 2009 - 06:12:33 CST)
- Re: [AMBER] Pseudoatoms David A. Case (Mon Mar 02 2009 - 17:25:29 CST)
  - [AMBER] How to restart the umbrella sampling jobs? Catein Catherine (Mon Mar 02 2009 - 23:52:16 CST)
    - RE: [AMBER] How to restart the umbrella sampling jobs? Ross Walker (Tue Mar 03 2009 - 10:00:04 CST)
    - Re: [AMBER] How to restart the umbrella sampling jobs? Gustavo Seabra (Tue Mar 03 2009 - 14:41:25 CST)
[AMBER] How can I use the charge I calculated (using mol2 file) ? ÀÌÀ±°æ (Mon Mar 02 2009 - 07:27:39 CST)
- Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? David A. Case (Mon Mar 02 2009 - 08:56:54 CST)
  - Re: Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? ÀÌÀ±°æ (Mon Mar 02 2009 - 19:39:37 CST)
    - Re: Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? David A. Case (Tue Mar 03 2009 - 07:39:26 CST)
    - Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? FyD (Tue Mar 03 2009 - 08:12:18 CST)
[AMBER] calculate shear viscosity oguz gurbulak (Mon Mar 02 2009 - 07:35:06 CST)
[AMBER] assigning velocities to each atom without heating the system Parimal Kar (Mon Mar 02 2009 - 10:44:26 CST)
- Re: [AMBER] assigning velocities to each atom without heating the system Gustavo Seabra (Mon Mar 02 2009 - 11:31:09 CST)
  - Re: [AMBER] assigning velocities to each atom without heating the system Parimal Kar (Mon Mar 02 2009 - 11:46:25 CST)
- RE: [AMBER] assigning velocities to each atom without heating the system Ross Walker (Mon Mar 02 2009 - 14:23:22 CST)
[AMBER] specification of antechamber AC file format? Nicholas Musolino (Tue Mar 03 2009 - 01:53:23 CST)
- Re: [AMBER] specification of antechamber AC file format? David A. Case (Wed Mar 04 2009 - 16:39:44 CST)
[AMBER] inpcrd and prmtop m m (Tue Mar 03 2009 - 03:27:06 CST)
- Re: [AMBER] inpcrd and prmtop Hannes Loeffler (Tue Mar 03 2009 - 03:37:16 CST)
  - RE: [AMBER] inpcrd and prmtop m m (Tue Mar 03 2009 - 04:08:51 CST)
  - Re: [AMBER] inpcrd and prmtop FyD (Tue Mar 03 2009 - 04:19:43 CST)
- Re: [AMBER] inpcrd and prmtop Gustavo Seabra (Tue Mar 03 2009 - 14:20:38 CST)
[AMBER] Fail to allocate ff Madhurima Jana (Tue Mar 03 2009 - 05:17:57 CST)
- Re: [AMBER] Fail to allocate ff Nicholas Musolino (Tue Mar 03 2009 - 07:10:21 CST)
  - Re: [AMBER] Fail to allocate ff Madhurima Jana (Tue Mar 03 2009 - 08:27:41 CST)
- Re: [AMBER] Fail to allocate ff Gustavo Seabra (Tue Mar 03 2009 - 14:36:53 CST)
[AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko (Tue Mar 03 2009 - 15:37:29 CST)
- Re: [AMBER] A good way to use an Amber force field with NAMD? Gustavo Seabra (Tue Mar 03 2009 - 18:08:33 CST)
  - Re: [AMBER] A good way to use an Amber force field with NAMD? Adrian Roitberg (Tue Mar 03 2009 - 18:11:49 CST)
[AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Jeff Schwinefus (Tue Mar 03 2009 - 16:18:25 CST)
- Re: [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Thomas Cheatham III (Wed Mar 04 2009 - 13:59:30 CST)
  - Re: [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Jeff Schwinefus (Wed Mar 04 2009 - 23:22:34 CST)
[AMBER] angle between ligand ring plane and axis Jia Xu (Wed Mar 04 2009 - 05:00:08 CST)
[AMBER] hydrogen bond . .. (Wed Mar 04 2009 - 05:12:33 CST)
- Re: [AMBER] hydrogen bond Carlos Simmerling (Wed Mar 04 2009 - 05:20:53 CST)
- RE: [AMBER] hydrogen bond Ross Walker (Wed Mar 04 2009 - 10:39:49 CST)
[AMBER] Regarding leap aneesh cna (Wed Mar 04 2009 - 05:43:52 CST)
- Re: [AMBER] Regarding leap Carlos Simmerling (Wed Mar 04 2009 - 05:48:30 CST)
- Re: [AMBER] Regarding leap Gustavo Seabra (Wed Mar 04 2009 - 16:05:25 CST)
  - Re: [AMBER] Regarding leap aneesh cna (Wed Mar 04 2009 - 22:29:17 CST)
    - Re: [AMBER] Regarding leap Gustavo Seabra (Thu Mar 05 2009 - 09:32:56 CST)
[AMBER] unning MMPBSA in CHCl3 environment SAFAK OZHAN (Wed Mar 04 2009 - 05:55:52 CST)
- Re: [AMBER] unning MMPBSA in CHCl3 environment Ray Luo (Wed Mar 04 2009 - 11:15:55 CST)
[AMBER] Thermodynamic Intergration problem Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 09:36:14 CST)
- RE: [AMBER] Thermodynamic Intergration problem Ross Walker (Wed Mar 04 2009 - 10:45:24 CST)
  - RE: [AMBER] Thermodynamic Intergration problem Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 11:00:06 CST)
[AMBER] Compilation and qmmm_div Benjamin Roberts (Wed Mar 04 2009 - 09:48:16 CST)
- RE: [AMBER] Compilation and qmmm_div Ross Walker (Wed Mar 04 2009 - 10:36:07 CST)
  - Re: [AMBER] Compilation and qmmm_div Benjamin Roberts (Wed Mar 04 2009 - 18:15:37 CST)
[AMBER] radial distribution function mask iccy liu (Wed Mar 04 2009 - 12:57:08 CST)
[AMBER] Segmentation faults Benjamin Roberts (Wed Mar 04 2009 - 18:17:50 CST)
Re: [AMBER] solvent and counter ions Bill Ross (Wed Mar 04 2009 - 18:20:45 CST)
[AMBER] DNA simulation: Problem with RMSD BERGY (Wed Mar 04 2009 - 21:44:26 CST)
- Re: [AMBER] DNA simulation: Problem with RMSD Thomas Cheatham (Wed Mar 04 2009 - 22:04:53 CST)
  - Re: [AMBER] DNA simulation: Problem with RMSD BERGY (Fri Mar 06 2009 - 00:20:00 CST)
[AMBER] Fwd: please help me out bharat lakhani (Wed Mar 04 2009 - 22:42:06 CST)
[AMBER] Re: Fw:How to creat .frcmod file FyD (Thu Mar 05 2009 - 00:22:56 CST)
[AMBER] please help me out bharat lakhani (Thu Mar 05 2009 - 02:35:44 CST)
- Re: [AMBER] please help me out FyD (Thu Mar 05 2009 - 03:22:20 CST)
  - Re: [AMBER] please help me out bharat lakhani (Thu Mar 05 2009 - 05:16:45 CST)
  - Re: [AMBER] please help me out bharat lakhani (Mon Mar 09 2009 - 00:04:45 CDT)
    - Re: [AMBER] please help me out FyD (Mon Mar 09 2009 - 03:10:08 CDT)
    - Re: [AMBER] please help me out bharat lakhani (Mon Mar 09 2009 - 03:43:08 CDT)
[AMBER] chemical shift penalty Jacopo Sgrignani (Thu Mar 05 2009 - 03:47:03 CST)
- Re: [AMBER] chemical shift penalty David A. Case (Thu Mar 05 2009 - 17:59:33 CST)
[AMBER] divcon error during antechamber run, convergence problem drugdesign (Thu Mar 05 2009 - 07:53:59 CST)
- Re: [AMBER] divcon error during antechamber run, convergence problem Martin Peters (Thu Mar 05 2009 - 08:21:19 CST)
- Re: [AMBER] divcon error during antechamber run, convergence problem Andrew Voronkov (Fri Mar 06 2009 - 12:04:55 CST)
  - Re: [AMBER] divcon error during antechamber run, convergence problem David A. Case (Fri Mar 06 2009 - 12:33:24 CST)
    - Re: [AMBER] divcon error during antechamber run, convergence problem Andrew Voronkov (Sat Mar 07 2009 - 09:58:19 CST)
[AMBER] secstruct Beale, John (Thu Mar 05 2009 - 07:54:20 CST)
- RE: [AMBER] secstruct Maxime Louet (Thu Feb 19 2009 - 08:17:17 CST)
  - Re: [AMBER] secstruct Carlos Simmerling (Thu Feb 19 2009 - 08:45:47 CST)
- Re: [AMBER] secstruct Carlos Simmerling (Thu Mar 05 2009 - 08:27:18 CST)
[AMBER] MM-PBSA decomp by residue and snapshot? Bradshaw, Richard (Thu Mar 05 2009 - 11:55:05 CST)
[AMBER] Warning: name change in pdb file residue Donald Keidel (Thu Mar 05 2009 - 13:25:38 CST)
- RE: [AMBER] Warning: name change in pdb file residue Duggan, Brendan M. (Thu Mar 05 2009 - 14:42:21 CST)
[AMBER] GBSA: dielectric symmetry Giacomo Bastianelli (Thu Mar 05 2009 - 17:29:50 CST)
- Re: [AMBER] GBSA: dielectric symmetry David A. Case (Thu Mar 05 2009 - 18:05:51 CST)
[AMBER] High RMSD for DNA: A to B transition study BERGY (Fri Mar 06 2009 - 01:26:57 CST)
- Re: [AMBER] High RMSD for DNA: A to B transition study David A. Case (Fri Mar 06 2009 - 08:57:02 CST)
  - Re: [AMBER] High RMSD for DNA: A to B transition study SENTHIL KUMAR (Fri Mar 13 2009 - 01:36:43 CDT)
    - Re: [AMBER] High RMSD for DNA: A to B transition study David A. Case (Fri Mar 13 2009 - 07:00:40 CDT)
[AMBER] Quality/size of HDD for Amber Francesco Pietra (Fri Mar 06 2009 - 03:26:03 CST)
- Re: [AMBER] Quality/size of HDD for Amber M. L. Dodson (Fri Mar 06 2009 - 09:44:45 CST)
  - Re: [AMBER] Quality/size of HDD for Amber Gustavo Seabra (Mon Mar 09 2009 - 12:44:54 CDT)
[AMBER] Solvate Box od amoeba water Hemant Gangwar (Fri Mar 06 2009 - 03:50:01 CST)
- Re: [AMBER] Solvate Box od amoeba water Wei Zhang (Fri Mar 06 2009 - 08:20:09 CST)
  - Re: [AMBER] Solvate Box od amoeba water Hemant Kumar (Sun Mar 22 2009 - 11:06:01 CDT)
[AMBER] catenan simulation problems Cristina Sisu (Fri Mar 06 2009 - 07:16:08 CST)
- Re: [AMBER] catenan simulation problems David A. Case (Fri Mar 06 2009 - 08:59:24 CST)
  - Re: [AMBER] catenan simulation problems Cristina Sisu (Fri Mar 06 2009 - 09:28:00 CST)
    - Re: [AMBER] catenan simulation problems David A. Case (Sat Mar 07 2009 - 17:25:07 CST)
    - Re: [AMBER] catenan simulation problems David A. Case (Wed Mar 18 2009 - 06:47:32 CDT)
  - Re: [AMBER] catenan simulation problems Cristina S.D. Sisu (Fri Mar 06 2009 - 09:35:46 CST)
[AMBER] Help with torsions in parm99.dat file Gregersen, Brent (Fri Mar 06 2009 - 16:44:17 CST)
- RE: [AMBER] Help with torsions in parm99.dat file Ross Walker (Fri Mar 06 2009 - 18:52:05 CST)
  - RE: [AMBER] Help with torsions in parm99.dat file Gregersen, Brent (Fri Mar 06 2009 - 20:15:11 CST)
    - RE: [AMBER] Help with torsions in parm99.dat file Ross Walker (Sat Mar 07 2009 - 00:32:23 CST)
  - Re: [AMBER] Help with torsions in parm99.dat file Astrid Maaß (Mon Mar 09 2009 - 08:27:30 CDT)
    - Re: [AMBER] Help with torsions in parm99.dat file Wei Zhang (Mon Mar 09 2009 - 09:38:56 CDT)
[AMBER] Problem with particle-mesh Ewald method Yunjie Zhao (Fri Mar 06 2009 - 21:29:02 CST)
- Re: [AMBER] Problem with particle-mesh Ewald method steinbrt_at_rci.rutgers.edu (Fri Mar 06 2009 - 21:42:26 CST)
- RE: [AMBER] Problem with particle-mesh Ewald method Ross Walker (Sat Mar 07 2009 - 00:10:34 CST)
[AMBER] analysis on Amber oguz gurbulak (Sat Mar 07 2009 - 12:04:19 CST)
- Re: [AMBER] analysis on Amber Thomas Cheatham (Sat Mar 07 2009 - 12:18:58 CST)
[AMBER] Fw:how to select force field Nancy (Sun Mar 08 2009 - 09:07:48 CDT)
- RE: [AMBER] Fw:how to select force field Ross Walker (Sun Mar 08 2009 - 12:52:56 CDT)
[AMBER] nmoldyn2 with Amber Adrien Delmont (Sun Mar 08 2009 - 09:37:40 CDT)
- Re: [AMBER] nmoldyn2 with Amber David Watson (Sun Mar 08 2009 - 09:54:57 CDT)
  - Re: [AMBER] nmoldyn2 with Amber M. L. Dodson (Sun Mar 08 2009 - 13:32:22 CDT)
    - Re: [AMBER] nmoldyn2 with Amber David Watson (Sun Mar 08 2009 - 15:00:39 CDT)
    - Re: [AMBER] nmoldyn2 with Amber Thomas Cheatham (Sun Mar 08 2009 - 15:10:17 CDT)
- Re: [AMBER] nmoldyn2 with Amber David Watson (Sun Mar 08 2009 - 10:02:55 CDT)
  - Re: [AMBER] nmoldyn2 with Amber M. L. Dodson (Sun Mar 08 2009 - 13:34:03 CDT)
[AMBER] addles segmentation fault gmail (Mon Mar 09 2009 - 03:28:56 CDT)
- Re: [AMBER] addles segmentation fault Carlos Simmerling (Mon Mar 09 2009 - 06:45:24 CDT)
  - Re: [AMBER] addles segmentation fault xiaonan zhang (Mon Mar 09 2009 - 08:08:47 CDT)
[AMBER] Particle-mesh Ewald method Yunjie Zhao (Mon Mar 09 2009 - 04:46:15 CDT)
- RE: [AMBER] Particle-mesh Ewald method Ross Walker (Mon Mar 09 2009 - 14:53:52 CDT)
[AMBER] 8Mureabox anna berteotti (Mon Mar 09 2009 - 05:07:52 CDT)
- Re: [AMBER] 8Mureabox David A. Case (Tue Mar 10 2009 - 07:51:08 CDT)
  - RE: [AMBER] 8Mureabox anna berteotti (Wed Mar 11 2009 - 03:45:03 CDT)
[AMBER] Restraint Mask length restriction !! Sampath Koppole (Mon Mar 09 2009 - 08:32:35 CDT)
- Re: [AMBER] Restraint Mask length restriction !! David A. Case (Mon Mar 09 2009 - 08:43:34 CDT)
- Re: [AMBER] Restraint Mask length restriction !! Sampath Koppole (Mon Mar 09 2009 - 09:06:23 CDT)
  - Re: [AMBER] Restraint Mask length restriction !! David A. Case (Mon Mar 09 2009 - 09:30:16 CDT)
- Re: [AMBER] Restraint Mask length restriction !! Sampath Koppole (Mon Mar 09 2009 - 09:39:38 CDT)
  - RE: [AMBER] Restraint Mask length restriction !! Ross Walker (Mon Mar 09 2009 - 14:50:08 CDT)
[AMBER] generalized distance restraint Rausch, Felix (Mon Mar 09 2009 - 08:48:01 CDT)
- Re: [AMBER] generalized distance restraint Carlos Simmerling (Mon Mar 09 2009 - 10:13:50 CDT)
  - RE: [AMBER] generalized distance restraint Rausch, Felix (Mon Mar 09 2009 - 11:15:11 CDT)
    - Re: [AMBER] generalized distance restraint Carlos Simmerling (Mon Mar 09 2009 - 11:39:43 CDT)
    - Re: [AMBER] generalized distance restraint M. L. Dodson (Mon Mar 09 2009 - 11:51:19 CDT)
- RE: [AMBER] generalized distance restraint Rausch, Felix (Wed Mar 11 2009 - 02:39:05 CDT)
[AMBER] Free Energy Decomposition Problem ozlem ulucan (Mon Mar 09 2009 - 08:55:45 CDT)
[AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Mon Mar 09 2009 - 19:12:27 CDT)
- RE: [AMBER] Changing Force Fields in "Midstream" Ross Walker (Mon Mar 09 2009 - 19:21:15 CDT)
  - RE: [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Tue Mar 10 2009 - 18:29:44 CDT)
  - RE: [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Wed Mar 11 2009 - 16:36:12 CDT)
[AMBER] problem in rmsd Parimal Kar (Mon Mar 09 2009 - 22:18:48 CDT)
- Re: [AMBER] problem in rmsd Thomas Cheatham (Mon Mar 09 2009 - 22:25:18 CDT)
  - Re: [AMBER] problem in rmsd Parimal Kar (Mon Mar 09 2009 - 22:36:13 CDT)
[AMBER] PB Bomb from MM-PBSA of Amber 10 Zhu, Yong-Liang (Mon Mar 09 2009 - 23:30:33 CDT)
- RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Wei Huang (Tue Mar 10 2009 - 05:30:50 CDT)
  - RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Zhu, Yong-Liang (Tue Mar 10 2009 - 11:06:43 CDT)
    - RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Wei Huang (Tue Mar 10 2009 - 11:20:29 CDT)
- RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Ray Luo (Tue Mar 10 2009 - 11:28:15 CDT)
[AMBER] sulfotyrosine parameters Ryan Pavlovicz (Tue Mar 10 2009 - 10:05:59 CDT)
[AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero (Tue Mar 10 2009 - 11:09:48 CDT)
- Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? David A. Case (Wed Mar 11 2009 - 06:08:17 CDT)
  - Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero (Wed Mar 11 2009 - 12:28:21 CDT)
[AMBER] about MD simulation ÁÎÇà»ª (Wed Mar 11 2009 - 04:19:28 CDT)
- Re: [AMBER] about MD simulation Carlos Simmerling (Wed Mar 11 2009 - 05:56:43 CDT)
  - å›žå¤ï¼š [AMBER] about MD simulation å»–é’åŽ (Wed Mar 11 2009 - 11:25:05 CDT)
[AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 07:44:17 CDT)
- RE: [AMBER] Seeking for suggestion related to plot the cluster out file Ross Walker (Wed Mar 11 2009 - 09:33:38 CDT)
  - Re: [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 09:57:40 CDT)
    - RE: [AMBER] Seeking for suggestion related to plot the cluster out file Ross Walker (Wed Mar 11 2009 - 10:55:38 CDT)
    - Re: [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 11:07:25 CDT)
[AMBER] installing AmberTools on Windows machines David A. Case (Wed Mar 11 2009 - 15:27:07 CDT)
[AMBER] polarizable force field and solvent zeinab bagheri (Wed Mar 11 2009 - 17:02:06 CDT)
[AMBER] Understanding the all.out file in the MM-PBSA output gmail (Wed Mar 11 2009 - 20:39:10 CDT)
- Re: [AMBER] Understanding the all.out file in the MM-PBSA output Hannes Kopitz (Thu Mar 12 2009 - 05:54:27 CDT)
  - RE: [AMBER] Understanding the all.out file in the MM-PBSA output Ray Luo (Thu Mar 12 2009 - 11:29:22 CDT)
[AMBER] polarizable force field and solvent zeinab bagheri (Thu Mar 12 2009 - 00:40:33 CDT)
[AMBER] Problem with REMD parul sharma (Thu Mar 12 2009 - 02:45:09 CDT)
- Re: [AMBER] Problem with REMD Carlos Simmerling (Thu Mar 12 2009 - 06:00:07 CDT)
[AMBER] Problems with MM-PBSA Calculation after MD German Erlenkamp (Thu Mar 12 2009 - 04:28:23 CDT)
- Re: [AMBER] Problems with MM-PBSA Calculation after MD Hannes Kopitz (Thu Mar 12 2009 - 06:06:54 CDT)
[AMBER] SMD in Amber10 Dmitri Nilov (Thu Mar 12 2009 - 13:12:13 CDT)
- Re: [AMBER] SMD in Amber10 Adrian Roitberg (Thu Mar 12 2009 - 13:46:14 CDT)
  - Re: [AMBER] SMD in Amber10 Dmitri Nilov (Fri Mar 13 2009 - 03:52:26 CDT)
[AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9 PRADEEP VENKATARAMAN (Thu Mar 12 2009 - 16:56:59 CDT)
- Re: [AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9 steinbrt_at_rci.rutgers.edu (Thu Mar 12 2009 - 19:37:08 CDT)
[AMBER] Problem running test.pmemd.AMOEBA mloureiro_at_cesga.es (Fri Mar 13 2009 - 06:45:30 CDT)
- [AMBER] Problem build pmemd Yiannis Georgiadis (Fri Mar 13 2009 - 19:14:49 CDT)
  - Re: [AMBER] Problem build pmemd Robert Duke (Fri Mar 13 2009 - 07:40:09 CDT)
  - Re: [AMBER] Problem build pmemd Atro Tossavainen (Sat Mar 14 2009 - 14:10:53 CDT)
- Re: [AMBER] Problem running test.pmemd.AMOEBA Robert Duke (Fri Mar 13 2009 - 09:33:55 CDT)
[AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 07:06:45 CDT)
[AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 09:43:45 CDT)
- Re: [AMBER] to understand multiplicity in antechamber Scott Brozell (Fri Mar 13 2009 - 14:05:06 CDT)
  - Re: [AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 17:43:28 CDT)
[AMBER] doubt-reg_ Targeted molecular dynamics balaji nagarajan (Fri Mar 13 2009 - 11:20:41 CDT)
[AMBER] problems compiling ambertool Per Jr. Greisen (Fri Mar 13 2009 - 14:08:36 CDT)
- Re: [AMBER] problems compiling ambertool David A. Case (Fri Mar 13 2009 - 14:54:56 CDT)
- Re: [AMBER] problems compiling ambertool Bill Ross (Mon Mar 16 2009 - 17:50:44 CDT)
  - Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Tue Mar 17 2009 - 03:10:20 CDT)
- Re: [AMBER] problems compiling ambertool Bill Ross (Tue Mar 17 2009 - 12:10:01 CDT)
- Re: [AMBER] problems compiling ambertool Bill Ross (Tue Mar 17 2009 - 12:24:48 CDT)
  - Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Wed Mar 18 2009 - 06:49:57 CDT)
[AMBER] suggestions for PB simulation Bala subramanian (Sat Mar 14 2009 - 11:41:19 CDT)
[AMBER] sander.MPI and pmemd.MPI in Fedora 8 John Bennett (Sun Mar 15 2009 - 16:23:16 CDT)
[AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 07:49:31 CDT)
[AMBER] about mm-pbsa å»–é’åŽ (Mon Mar 16 2009 - 09:59:40 CDT)
[AMBER] about mm-pbsa å»–é’åŽ (Mon Mar 16 2009 - 10:02:49 CDT)
- RE: [AMBER] about mm-pbsa Wei Huang (Mon Mar 16 2009 - 10:17:30 CDT)
[AMBER] minimisation with igb=10 Bala subramanian (Mon Mar 16 2009 - 10:43:10 CDT)
- Re: [AMBER] minimisation with igb=10 Carlos Simmerling (Mon Mar 16 2009 - 10:45:47 CDT)
  - Re: [AMBER] minimisation with igb=10 Bala subramanian (Mon Mar 16 2009 - 10:56:48 CDT)
    - Re: [AMBER] minimisation with igb=10 Carlos Simmerling (Mon Mar 16 2009 - 11:04:37 CDT)
    - RE: [AMBER] minimisation with igb=10 Ray Luo (Mon Mar 16 2009 - 11:34:21 CDT)
[AMBER] Actual force constant in SMD Dmitri Nilov (Mon Mar 16 2009 - 13:07:09 CDT)
[AMBER] Re: join two units in amber9 or amber10 Taufik Al-Sarraj (Mon Mar 16 2009 - 16:11:30 CDT)
Re: [AMBER] Re: join two units in amber9 or amber10 Bill Ross (Mon Mar 16 2009 - 17:56:01 CDT)
[AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 20:02:09 CDT)
[AMBER] Input file of the second stage RESP fitting Cen Gao (Mon Mar 16 2009 - 23:29:17 CDT)
- Re: [AMBER] Input file of the second stage RESP fitting FyD (Tue Mar 17 2009 - 08:32:58 CDT)
  - Re: [AMBER] Input file of the second stage RESP fitting Cen Gao (Tue Mar 17 2009 - 16:24:24 CDT)
[AMBER] regarding tutorial on united atom force field jani sahil (Mon Mar 16 2009 - 23:51:16 CDT)
- Re: [AMBER] regarding tutorial on united atom force field Ray Luo (Tue Mar 17 2009 - 11:22:01 CDT)
[AMBER] need- help-for TMD balaji nagarajan (Tue Mar 17 2009 - 00:16:34 CDT)
[AMBER] Unit 5 Error on OPEN: nan.in Nancy (Tue Mar 17 2009 - 04:11:10 CDT)
- Re: [AMBER] Unit 5 Error on OPEN: nan.in mathew k varghese (Mon Mar 16 2009 - 08:36:57 CDT)
  - Re:Re: [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 09:01:14 CDT)
    - Re: Re: [AMBER] Unit 5 Error on OPEN: nan.in Carlos Simmerling (Mon Mar 16 2009 - 09:32:02 CDT)
- Re: [AMBER] Unit 5 Error on OPEN: nan.in mathew k varghese (Tue Mar 17 2009 - 06:22:08 CDT)
  - Re: [AMBER] Unit 5 Error on OPEN: nan.in Jenny Iskrenova (Tue Mar 17 2009 - 07:34:00 CDT)
  - Re:Re: [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Tue Mar 17 2009 - 08:37:44 CDT)
[AMBER] removing center of mass Bala subramanian (Tue Mar 17 2009 - 10:21:28 CDT)
[AMBER] convert .mol2 file to .pdb with atomtype definitions Pansy Patel (Tue Mar 17 2009 - 10:50:57 CDT)
- Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions David A. Case (Tue Mar 17 2009 - 11:00:19 CDT)
  - Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions Pansy Patel (Tue Mar 17 2009 - 11:09:10 CDT)
    - Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions Wei Zhang (Tue Mar 17 2009 - 11:33:27 CDT)
    - RE: [AMBER] convert .mol2 file to .pdb with atomtype definitions Pankaj R. Daga (Tue Mar 17 2009 - 11:41:20 CDT)
[AMBER] temperature rises with igb=1 Bala subramanian (Tue Mar 17 2009 - 11:35:41 CDT)
- Re: [AMBER] temperature rises with igb=1 Carlos Simmerling (Tue Mar 17 2009 - 11:44:32 CDT)
- RE: [AMBER] temperature rises with igb=1 Ross Walker (Tue Mar 17 2009 - 11:53:04 CDT)
  - Re: [AMBER] temperature rises with igb=1 Carlos Simmerling (Tue Mar 17 2009 - 11:58:05 CDT)
    - Re: [AMBER] temperature rises with igb=1 Bala subramanian (Thu Mar 19 2009 - 06:24:45 CDT)
    - Re: [AMBER] temperature rises with igb=1 David A. Case (Thu Mar 19 2009 - 07:04:54 CDT)
Re: [AMBER] Unit 5 Error on OPEN: nan.in Bill Ross (Tue Mar 17 2009 - 12:12:07 CDT)
[AMBER] CCL4 simulation sudipta (Tue Mar 17 2009 - 13:18:07 CDT)
- Re: [AMBER] CCL4 simulation David A. Case (Tue Mar 17 2009 - 21:14:51 CDT)
  - Re: [AMBER] CCL4 simulation sudipta (Wed Mar 18 2009 - 02:47:48 CDT)
    - Re: [AMBER] CCL4 simulation David A. Case (Wed Mar 18 2009 - 06:06:30 CDT)
[AMBER] error in constructing DNA from nucgen Pansy Patel (Tue Mar 17 2009 - 13:43:49 CDT)
- Re: [AMBER] error in constructing DNA from nucgen Carlos Simmerling (Tue Mar 17 2009 - 13:53:05 CDT)
  - Re: [AMBER] error in constructing DNA from nucgen Pansy Patel (Tue Mar 17 2009 - 14:24:58 CDT)
    - RE: [AMBER] error in constructing DNA from nucgen Ross Walker (Tue Mar 17 2009 - 14:31:16 CDT)
- Re: [AMBER] error in constructing DNA from nucgen Carlos Simmerling (Tue Mar 17 2009 - 13:53:05 CDT)
- Re: [AMBER] error in constructing DNA from nucgen Carlos Simmerling (Tue Mar 17 2009 - 13:53:05 CDT)
- Re: [AMBER] error in constructing DNA from nucgen Bill Ross (Tue Mar 17 2009 - 17:47:07 CDT)
[AMBER] TMD balaji nagarajan (Tue Mar 17 2009 - 23:58:37 CDT)
- Re: [AMBER] TMD Carlos Simmerling (Wed Mar 18 2009 - 05:32:14 CDT)
  - RE: [AMBER] TMD balaji nagarajan (Wed Mar 18 2009 - 06:15:55 CDT)
[AMBER] About error of "vertex atom mismatch" å»–é’åŽ (Wed Mar 18 2009 - 03:30:29 CDT)
[AMBER] errors about install amber9 on MAC OS zgong.hust (Wed Mar 18 2009 - 03:41:19 CDT)
- Re: [AMBER] errors about install amber9 on MAC OS David A. Case (Wed Mar 18 2009 - 06:08:44 CDT)
[AMBER] protein protrudes from unit cell Jeffrey (Wed Mar 18 2009 - 03:59:06 CDT)
- Re: [AMBER] protein protrudes from unit cell Hannes Loeffler (Wed Mar 18 2009 - 04:08:41 CDT)
- RE: [AMBER] protein protrudes from unit cell Ross Walker (Wed Mar 18 2009 - 10:39:23 CDT)
  - Re: [AMBER] protein protrudes from unit cell Carlos Simmerling (Wed Mar 18 2009 - 10:49:43 CDT)
[AMBER] sleap and check Alan (Wed Mar 18 2009 - 06:18:27 CDT)
- Re: [AMBER] sleap and check Wei Zhang (Wed Mar 18 2009 - 09:40:57 CDT)
  - Re: [AMBER] sleap and check Alan (Wed Mar 18 2009 - 16:23:51 CDT)
[AMBER] Mass of LP PRADEEP VENKATARAMAN (Wed Mar 18 2009 - 22:27:24 CDT)
- Re: [AMBER] Mass of LP David A. Case (Thu Mar 19 2009 - 06:27:48 CDT)
[AMBER] simulation in water-oil (or water/hydrophobic-solvent) box ranga nath (Wed Mar 18 2009 - 23:27:54 CDT)
- Re: [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box David A. Case (Thu Mar 19 2009 - 12:38:52 CDT)
  - [AMBER] protein PDB Chih-Ying Lin (Thu Mar 19 2009 - 15:43:15 CDT)
  - Re: [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box ranga nath (Sat Mar 21 2009 - 21:04:13 CDT)
[AMBER] Metal in MD simulation priya priya (Thu Mar 19 2009 - 01:25:09 CDT)
- Re: [AMBER] Metal in MD simulation Jagadeesh, M.N., Ph.D. (Thu Mar 19 2009 - 09:48:28 CDT)
- RE: [AMBER] Metal in MD simulation Ross Walker (Thu Mar 19 2009 - 10:12:24 CDT)
- Re: [AMBER] Metal in MD simulation Bill Ross (Thu Mar 19 2009 - 16:22:12 CDT)
- Re: [AMBER] Metal in MD simulation priya priya (Fri Mar 20 2009 - 01:15:06 CDT)
[AMBER] About mm-pbsa å»–é’åŽ (Thu Mar 19 2009 - 01:48:21 CDT)
[AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy? Youn Kyeung Lee (Thu Mar 19 2009 - 02:31:16 CDT)
- Re: [AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy? FyD (Sun Mar 22 2009 - 15:12:17 CDT)
[AMBER] error for nmode Dechang Li (Thu Mar 19 2009 - 06:00:09 CDT)
- Re: [AMBER] error for nmode David A. Case (Thu Mar 19 2009 - 06:31:24 CDT)
[AMBER] pmemd compile error.... Giorgos Lamprinidis (Thu Mar 19 2009 - 10:06:04 CDT)
- Re: [AMBER] pmemd compile error.... Robert Duke (Thu Mar 19 2009 - 10:24:29 CDT)
  - Re: [AMBER] pmemd compile error.... Yiannis Georgiadis (Tue Mar 24 2009 - 15:10:27 CDT)
    - Re: [AMBER] pmemd compile error.... case (Tue Mar 24 2009 - 07:12:46 CDT)
    - Re: [AMBER] pmemd compile error.... Robert Duke (Tue Mar 24 2009 - 07:19:45 CDT)
- Re: [AMBER] pmemd compile error.... Robert Duke (Thu Mar 19 2009 - 10:25:04 CDT)
[AMBER] Parametrisation of Silicon based molecules for Amber simulations ? Marek Malý (Thu Mar 19 2009 - 18:49:21 CDT)
- [AMBER] FF Parameters Transformations ...? Marek Malý (Wed Apr 01 2009 - 12:29:26 CDT)
  - Re: [AMBER] FF Parameters Transformations ...? Karl Kirschner (Mon Apr 06 2009 - 02:39:31 CDT)
    - Re: [AMBER] FF Parameters Transformations ...? Marek Malý (Mon Apr 06 2009 - 15:03:58 CDT)
[AMBER] analysing DNA trajectory balaji nagarajan (Fri Mar 20 2009 - 00:09:10 CDT)
- Re: [AMBER] analysing DNA trajectory Bala subramanian (Fri Mar 20 2009 - 03:06:08 CDT)
[AMBER] Help needed in amber parallel installation sushobhan_at_iiar.res.in (Fri Mar 20 2009 - 01:39:36 CDT)
- Re: [AMBER] Help needed in amber parallel installation Carlos Simmerling (Fri Mar 20 2009 - 06:34:31 CDT)
- RE: [AMBER] Help needed in amber parallel installation Ross Walker (Fri Mar 20 2009 - 10:40:30 CDT)
[AMBER] QM/MM charges Jacopo Sgrignani (Fri Mar 20 2009 - 04:38:30 CDT)
- RE: [AMBER] QM/MM charges Ross Walker (Fri Mar 20 2009 - 10:37:34 CDT)
[AMBER] Announcement of Model(l)ing'09 - The annual 2009 MGMS Meeting in Erlangen, Germany Harald Lanig (Fri Mar 20 2009 - 06:25:09 CDT)
[AMBER] MMGBSA IG Value Rajesh Raju (Fri Mar 20 2009 - 12:20:52 CDT)
- Re: [AMBER] MMGBSA IG Value Carlos Simmerling (Fri Mar 20 2009 - 12:25:38 CDT)
  - Re: [AMBER] MMGBSA IG Value Rajesh Raju (Fri Mar 20 2009 - 12:36:37 CDT)
    - Re: [AMBER] MMGBSA IG Value Carlos Simmerling (Fri Mar 20 2009 - 12:42:14 CDT)
[AMBER] xmgrace Nancy (Fri Mar 20 2009 - 23:41:33 CDT)
- Re: [AMBER] xmgrace mathew k varghese (Sat Mar 21 2009 - 00:18:32 CDT)
  - Re:Re: [AMBER] xmgrace Nancy (Sat Mar 21 2009 - 00:42:48 CDT)
[AMBER] adding chain id to ptraj pdb output Paul Brandt (Sat Mar 21 2009 - 21:09:59 CDT)
- Re: [AMBER] adding chain id to ptraj pdb output Bala subramanian (Mon Mar 23 2009 - 06:37:43 CDT)
- Re: [AMBER] adding chain id to ptraj pdb output Joe Krahn (Mon Mar 23 2009 - 18:20:30 CDT)
[AMBER] about mm-pbsa å»–é’åŽ (Mon Mar 23 2009 - 04:10:29 CDT)
[AMBER] leap and chirality Karl Kirschner (Mon Mar 23 2009 - 04:54:29 CDT)
- Re: [AMBER] leap and chirality David A. Case (Mon Mar 23 2009 - 08:16:14 CDT)
  - Re: [AMBER] leap and chirality Karl Kirschner (Mon Mar 23 2009 - 09:05:56 CDT)
[AMBER] problem in installing AMBER10 Dr. Debaprasad Giri (Mon Mar 23 2009 - 05:31:26 CDT)
- Re: [AMBER] problem in installing AMBER10 David A. Case (Mon Mar 23 2009 - 06:07:17 CDT)
  - Re: [AMBER] problem in installing AMBER10 Dr. Debaprasad Giri (Fri Mar 27 2009 - 05:16:47 CDT)
    - Re: [AMBER] problem in installing AMBER10 David A. Case (Fri Mar 27 2009 - 07:05:31 CDT)
    - Re: [AMBER] problem in installing AMBER10 Dr. Debaprasad Giri (Sat Apr 04 2009 - 07:13:46 CDT)
[AMBER] Regarding use of PME along with Implict solvation jani sahil (Mon Mar 23 2009 - 05:38:39 CDT)
- Re: [AMBER] Regarding use of PME along with Implict solvation parul sharma (Mon Mar 23 2009 - 05:55:24 CDT)
  - Re: [AMBER] Regarding use of PME along with Implict solvation jani sahil (Mon Mar 23 2009 - 08:04:15 CDT)
[AMBER] helical parameters balaji nagarajan (Mon Mar 23 2009 - 11:21:04 CDT)
- Re: [AMBER] helical parameters Bala subramanian (Mon Mar 23 2009 - 13:14:29 CDT)
[AMBER] pmemd compile error Giorgos Lamprinidis (Mon Mar 23 2009 - 15:54:37 CDT)
- Re: [AMBER] pmemd compile error Robert Duke (Mon Mar 23 2009 - 16:03:45 CDT)
[AMBER] errors on reading time series file in WHAM calculation gmail (Mon Mar 23 2009 - 19:35:02 CDT)
- Re: [AMBER] errors on reading time series file in WHAM calculation Jenny Iskrenova (Tue Mar 24 2009 - 09:35:51 CDT)
[AMBER] validation of parameters and request of suggestions Jeffrey (Mon Mar 23 2009 - 21:16:35 CDT)
[AMBER] continuam water Mannan (Mon Mar 23 2009 - 23:11:50 CDT)
- Re: [AMBER] continuam water Carlos Simmerling (Tue Mar 24 2009 - 08:36:15 CDT)
  - [AMBER] POLARIZABLE WATER MODEL CHAMI F. (Tue Mar 24 2009 - 13:03:25 CDT)
[AMBER] change in protein ligand order Hannes Wallnoefer (Tue Mar 24 2009 - 06:05:36 CDT)
- Re: [AMBER] change in protein ligand order Hannes Loeffler (Tue Mar 24 2009 - 06:27:24 CDT)
  - Re: [AMBER] change in protein ligand order Hannes Wallnoefer (Tue Mar 24 2009 - 07:38:18 CDT)
- Re: [AMBER] change in protein ligand order Bill Ross (Tue Mar 24 2009 - 13:07:42 CDT)
  - Re: [AMBER] change in protein ligand order Hannes Wallnoefer (Tue Mar 24 2009 - 15:45:16 CDT)
[AMBER] validation of parameters and request suggestions Jeffrey (Tue Mar 24 2009 - 06:52:19 CDT)
[AMBER] create new crd files from transformed coordinates Donald Keidel (Tue Mar 24 2009 - 20:49:03 CDT)
- Re: [AMBER] create new crd files from transformed coordinates case (Wed Mar 25 2009 - 07:26:29 CDT)
[AMBER] question about pair wise per-residue energy decomposition; idecomp=3 wfli_at_biophy.nju.edu.cn (Wed Mar 25 2009 - 04:48:29 CDT)
- Re: [AMBER] question about pair wise per-residue energy decomposition; idecomp=3 case (Wed Mar 25 2009 - 13:58:02 CDT)
[AMBER] About Free energy decomposition Rajesh Raju (Wed Mar 25 2009 - 09:08:00 CDT)
[AMBER] Rosetta Academic Training Webinar Nir London (Wed Mar 25 2009 - 11:14:21 CDT)
[AMBER] How to reproduce a parallel PMEMD run? Siang Yip (Wed Mar 25 2009 - 17:33:56 CDT)
- Re: [AMBER] How to reproduce a parallel PMEMD run? Robert Duke (Wed Mar 25 2009 - 18:45:49 CDT)
[AMBER] Amber 10 and core i7 Supat Jiranusornkul (Thu Mar 26 2009 - 04:13:10 CDT)
[AMBER] To find radial distribution curve nicholus bhattacharjee (Thu Mar 26 2009 - 12:16:07 CDT)
[AMBER] installing resp on linux 64bit aditya chhikara (Thu Mar 26 2009 - 12:24:27 CDT)
- Re: [AMBER] installing resp on linux 64bit FyD (Thu Mar 26 2009 - 14:37:22 CDT)
  - Re: [AMBER] installing resp on linux 64bit aditya chhikara (Thu Mar 26 2009 - 16:36:50 CDT)
[AMBER] Problem with "Atom does not have a type" Richard Tseng (Thu Mar 26 2009 - 18:17:19 CDT)
- Re: [AMBER] Problem with "Atom does not have a type" David A. Case (Fri Mar 27 2009 - 06:44:22 CDT)
  - Re: [AMBER] Problem with "Atom does not have a type" Richard Tseng (Fri Mar 27 2009 - 16:51:32 CDT)
[AMBER] Fwd: AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Thu Mar 26 2009 - 18:44:59 CDT)
- Re: [AMBER] Fwd: AMBER: MM-PBSA in AMBER 10 Ray Luo (Thu Mar 26 2009 - 18:54:17 CDT)
[AMBER] Problem reading PDB file into XLEAP Hopkins, Robert (Thu Mar 26 2009 - 19:01:26 CDT)
- Re: [AMBER] Problem reading PDB file into XLEAP David A. Case (Fri Mar 27 2009 - 07:39:26 CDT)
  - RE: [AMBER] Problem reading PDB file into XLEAP Hopkins, Robert (Fri Mar 27 2009 - 17:09:11 CDT)
[AMBER] Antechamber problem Å·ÑôµÂ·½ (Thu Mar 26 2009 - 23:44:24 CDT)
- Re: [AMBER] Antechamber problem David A. Case (Fri Mar 27 2009 - 07:29:48 CDT)
- Re: [AMBER] Antechamber problem Junmei Wang (Fri Mar 27 2009 - 16:21:33 CDT)
  - RE: [AMBER] Antechamber problem Å·ÑôµÂ·½ (Fri Mar 27 2009 - 19:55:03 CDT)
[AMBER] problem using amoeba Hemant Gangwar (Fri Mar 27 2009 - 05:41:26 CDT)
- Re: [AMBER] problem using amoeba Robert Duke (Fri Mar 27 2009 - 07:22:31 CDT)
[AMBER] Question Kshatresh Dutta Dubey (Fri Mar 27 2009 - 08:06:09 CDT)
- RE: [AMBER] Question Rausch, Felix (Fri Mar 27 2009 - 08:37:29 CDT)
  - Re: [AMBER] Question Kshatresh Dutta Dubey (Sat Mar 28 2009 - 04:16:03 CDT)
    - Re: [AMBER] Question David A. Case (Sat Mar 28 2009 - 08:38:49 CDT)
- [AMBER] BINDER/xaLeap Taufik Al-Sarraj (Mon Mar 30 2009 - 20:00:10 CDT)
  - RE: [AMBER] BINDER/xaLeap Ross Walker (Mon Mar 30 2009 - 20:29:46 CDT)
[AMBER] PMEMD 9 on MVAPICH / Infiniband problem Nick Holway (Fri Mar 27 2009 - 10:55:38 CDT)
- RE: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem Ross Walker (Fri Mar 27 2009 - 20:04:04 CDT)
  - Re: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem fohm fohm (Tue Mar 31 2009 - 06:04:10 CDT)
    - Re: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem Robert Duke (Tue Mar 31 2009 - 07:21:22 CDT)
[AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Fri Mar 27 2009 - 21:30:04 CDT)
- Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case (Sat Mar 28 2009 - 16:39:35 CDT)
- Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Sat Mar 28 2009 - 20:17:21 CDT)
  - Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case (Sat Mar 28 2009 - 21:26:58 CDT)
- Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Sat Mar 28 2009 - 22:07:47 CDT)
- Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Sat Mar 28 2009 - 23:00:00 CDT)
  - Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case (Sun Mar 29 2009 - 13:41:13 CDT)
[AMBER] .rst file generation problem. Aravind S (Mon Mar 30 2009 - 00:48:55 CDT)
- Re: [AMBER] .rst file generation problem. Aravind S (Mon Mar 30 2009 - 01:32:12 CDT)
- Re: [AMBER] .rst file generation problem. Carlos Simmerling (Mon Mar 30 2009 - 06:30:58 CDT)
- Re: [AMBER] .rst file generation problem. Aravind S (Tue Mar 31 2009 - 03:49:17 CDT)
  - Re: [AMBER] .rst file generation problem. Carlos Simmerling (Tue Mar 31 2009 - 06:28:35 CDT)
[AMBER] "rfree: End of file on unit 5" Remya S R (Mon Mar 30 2009 - 01:21:53 CDT)
- Re: [AMBER] "rfree: End of file on unit 5" mathew k varghese (Mon Mar 30 2009 - 04:57:44 CDT)
[AMBER] mm_pbsa problem Giorgos Lamprinidis (Mon Mar 30 2009 - 05:02:07 CDT)
- Re: [AMBER] mm_pbsa problem case (Mon Mar 30 2009 - 07:48:05 CDT)
  - Re: [AMBER] mm_pbsa problem Giorgos Lamprinidis (Mon Mar 30 2009 - 08:59:55 CDT)
    - RE: [AMBER] mm_pbsa problem Ray Luo (Mon Mar 30 2009 - 12:27:59 CDT)
    - Re: [AMBER] mm_pbsa problem Giorgos Lamprinidis (Wed Apr 01 2009 - 02:36:53 CDT)
[AMBER] Creating conditions for biased MD Francesco Pietra (Mon Mar 30 2009 - 05:16:54 CDT)
- Re: [AMBER] Creating conditions for biased MD Carlos Simmerling (Mon Mar 30 2009 - 06:56:36 CDT)
  - Re: [AMBER] Creating conditions for biased MD Francesco Pietra (Mon Apr 20 2009 - 12:31:52 CDT)
- Re: [AMBER] Creating conditions for biased MD Bill Ross (Wed Apr 22 2009 - 11:19:20 CDT)
  - Re: [AMBER] Creating conditions for biased MD Francesco Pietra (Wed Apr 22 2009 - 13:01:39 CDT)
[AMBER] amber tools installation Jayalakshmi Sridhar (Mon Mar 30 2009 - 10:44:57 CDT)
- Re: [AMBER] amber tools installation case (Mon Mar 30 2009 - 11:28:38 CDT)
[AMBER] Announcing NMR validation web interface iCing Alan (Mon Mar 30 2009 - 11:55:00 CDT)
[AMBER] problem with the results in the .out file! Aravind S (Tue Mar 31 2009 - 00:30:57 CDT)
- Re: [AMBER] problem with the results in the .out file! Gustavo Seabra (Tue Mar 31 2009 - 08:01:41 CDT)
  - Re: [AMBER] problem with the results in the .out file! Aravind S (Thu Apr 02 2009 - 00:49:19 CDT)
[AMBER] how to convert secstruct output file into plot or pictorial representation Siddharth Rastogi (Tue Mar 31 2009 - 05:56:37 CDT)
[AMBER] modifying LYN Marius Retegan (Tue Mar 31 2009 - 08:36:21 CDT)
- Re: [AMBER] modifying LYN FyD (Tue Mar 31 2009 - 10:41:56 CDT)
  - Re: [AMBER] modifying LYN Marius Retegan (Tue Mar 31 2009 - 11:58:06 CDT)
[AMBER] combine many coord files into trajectory file Peter Gannett (Tue Mar 31 2009 - 08:51:16 CDT)
- Re: [AMBER] combine many coord files into trajectory file Carlos Simmerling (Tue Mar 31 2009 - 08:55:58 CDT)
  - Re: [AMBER] combine many coord files into trajectory file Peter Gannett (Tue Mar 31 2009 - 09:25:00 CDT)
[AMBER] Maxwell-Boltzmann distribution and ig=-1 Naser Alijabbari (Tue Mar 31 2009 - 20:35:43 CDT)
- Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Carlos Simmerling (Tue Mar 31 2009 - 20:41:49 CDT)
  - Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Naser Alijabbari (Tue Mar 31 2009 - 21:15:13 CDT)
[AMBER] a layer of water Nancy (Tue Mar 31 2009 - 20:37:51 CDT)
- Re: [AMBER] a layer of water oguz gurbulak (Wed Apr 01 2009 - 02:26:46 CDT)
[AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation Therese Malliavin (Wed Apr 01 2009 - 04:06:19 CDT)
- Re: [AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation David A. Case (Sat Apr 04 2009 - 08:20:28 CDT)
[AMBER] run protein with structural Ca+ sarah genare (Wed Apr 01 2009 - 06:01:24 CDT)
[AMBER] Failure to compile amber9 serial ifort gcc Francesco Pietra (Wed Apr 01 2009 - 06:04:18 CDT)
- Re: [AMBER] Failure to compile amber9 serial ifort gcc Alessandro Nascimento (Wed Apr 01 2009 - 06:09:42 CDT)
- Re: [AMBER] Failure to compile amber9 serial ifort gcc Francesco Pietra (Thu Apr 02 2009 - 06:16:36 CDT)
  - RE: [AMBER] Failure to compile amber9 serial ifort gcc Ross Walker (Thu Apr 02 2009 - 10:45:19 CDT)
    - Re: [AMBER] Failure to compile amber9 serial ifort gcc Francesco Pietra (Thu Apr 02 2009 - 11:00:46 CDT)
[AMBER] fillratio error in mmpbsa m m (Wed Apr 01 2009 - 06:42:45 CDT)
- Re: [AMBER] fillratio error in mmpbsa Han Ming (Wed Apr 01 2009 - 10:06:08 CDT)
- RE: [AMBER] fillratio error in mmpbsa Ray Luo (Wed Apr 01 2009 - 14:24:20 CDT)
[AMBER] calculation of Pi-Pi interaction energy aneesh cna (Wed Apr 01 2009 - 07:01:51 CDT)
[AMBER] calculation of Pi-Pi interaction energy Jacopo Sgrignani (Wed Apr 01 2009 - 07:24:28 CDT)
- Re: [AMBER] calculation of Pi-Pi interaction energy Jiri Sponer (Wed Apr 01 2009 - 07:38:49 CDT)
[AMBER] yacc parser Francesco Pietra (Wed Apr 01 2009 - 09:58:01 CDT)
- Re: [AMBER] yacc parser Mark Williamson (Wed Apr 01 2009 - 12:15:56 CDT)
- [AMBER] Fwd: yacc parser Francesco Pietra (Wed Apr 01 2009 - 15:53:01 CDT)
- Re: [AMBER] yacc parser David A. Case (Thu Apr 02 2009 - 07:03:06 CDT)
  - Re: [AMBER] yacc parser Francesco Pietra (Thu Apr 02 2009 - 10:37:53 CDT)
[AMBER] make test.serial.QMMM michael bane (Wed Apr 01 2009 - 10:44:51 CDT)
- Re: [AMBER] make test.serial.QMMM Seth Hayik (Wed Apr 01 2009 - 12:26:21 CDT)
[AMBER] ptraj and namd charmm dcd Sandro L. Fornili (Wed Apr 01 2009 - 10:59:37 CDT)
- Re: [AMBER] ptraj and namd charmm dcd Thomas Cheatham III (Wed Apr 01 2009 - 11:08:51 CDT)
[AMBER] AmberTools compilation error Kijeong Kwac (Wed Apr 01 2009 - 14:04:00 CDT)
- Re: [AMBER] AmberTools compilation error Marius Retegan (Wed Apr 01 2009 - 15:03:59 CDT)
[AMBER] Help: An error happened when I calculate mm/pbsa thirsty (Thu Apr 02 2009 - 03:12:25 CDT)
- Re: [AMBER] Help: An error happened when I calculate mm/pbsa Carlos Simmerling (Thu Apr 02 2009 - 06:19:04 CDT)
  - Re: [AMBER] Help: An error happened when I calculate mm/pbsa thirsty (Fri Apr 03 2009 - 02:11:19 CDT)
[AMBER] Umbrella test Arnaud (Thu Apr 02 2009 - 04:51:01 CDT)
- Re: [AMBER] Umbrella test David A. Case (Sat Apr 04 2009 - 08:12:13 CDT)
[AMBER] please help me out bharat lakhani (Thu Apr 02 2009 - 05:13:48 CDT)
- Re: [AMBER] please help me out David A. Case (Thu Apr 02 2009 - 12:48:10 CDT)
[AMBER] Counter-ions waleed zalloum (Thu Apr 02 2009 - 05:15:12 CDT)
[AMBER] problem in input balaji nagarajan (Thu Apr 02 2009 - 05:29:39 CDT)
- RE: [AMBER] problem in input Rausch, Felix (Thu Apr 02 2009 - 06:08:27 CDT)
  - RE: [AMBER] problem in input balaji nagarajan (Thu Apr 02 2009 - 15:23:18 CDT)
    - RE: [AMBER] problem in input Rausch, Felix (Fri Apr 03 2009 - 03:04:36 CDT)
[AMBER] number of waters in first and second solvation shell Siddharth Rastogi (Thu Apr 02 2009 - 06:40:21 CDT)
[AMBER] explicit ion with igb=1 Bala subramanian (Thu Apr 02 2009 - 08:39:10 CDT)
- Re: [AMBER] explicit ion with igb=1 Carlos Simmerling (Thu Apr 02 2009 - 08:53:54 CDT)
[AMBER] Averaging simulations Naser Alijabbari (Thu Apr 02 2009 - 10:21:41 CDT)
- Re: [AMBER] Averaging simulations Carlos Simmerling (Thu Apr 02 2009 - 10:24:28 CDT)
[AMBER] Error in trajin and rms Pansy Patel (Thu Apr 02 2009 - 13:58:47 CDT)
- Re: [AMBER] Error in trajin and rms Carlos Simmerling (Thu Apr 02 2009 - 14:19:39 CDT)
- RE: [AMBER] Error in trajin and rms iccy liu (Thu Apr 02 2009 - 14:19:16 CDT)
  - RE: [AMBER] Error in trajin and rms Pansy Patel (Thu Apr 02 2009 - 14:25:58 CDT)
[AMBER] parallel installation of amber on sun Per Jr. Greisen (Thu Apr 02 2009 - 14:02:47 CDT)
- Re: [AMBER] parallel installation of amber on sun Atro Tossavainen (Thu Apr 02 2009 - 15:23:05 CDT)
  - Re: [AMBER] parallel installation of amber on sun Per Jr. Greisen (Thu Apr 02 2009 - 15:38:54 CDT)
- Re: [AMBER] parallel installation of amber on sun Atro Tossavainen (Fri Apr 03 2009 - 04:39:25 CDT)
  - Re: [AMBER] parallel installation of amber on sun Per Jr. Greisen (Fri Apr 03 2009 - 05:22:45 CDT)
    - Re: [AMBER] parallel installation of amber on sun Atro Tossavainen (Fri Apr 03 2009 - 16:40:42 CDT)
    - Re: [AMBER] parallel installation of amber on sun Atro Tossavainen (Fri Apr 03 2009 - 17:33:52 CDT)
[AMBER] long polymer chain and image command in ptraj iccy liu (Thu Apr 02 2009 - 14:11:26 CDT)
- Re: [AMBER] long polymer chain and image command in ptraj Karl Kirschner (Mon Apr 06 2009 - 03:15:00 CDT)
[AMBER] Contour plot Beale, John (Thu Apr 02 2009 - 14:31:22 CDT)
- Re: [AMBER] Contour plot Gustavo Seabra (Thu Apr 02 2009 - 14:47:14 CDT)
[AMBER] How to delete the frames at specific intervals Mannan (Thu Apr 02 2009 - 20:16:49 CDT)
- Re: [AMBER] How to delete the frames at specific intervals Bala subramanian (Fri Apr 03 2009 - 04:55:35 CDT)
[AMBER] How to find out residence time of water molecules Mannan (Thu Apr 02 2009 - 20:52:36 CDT)
- Re: [AMBER] How to find out residence time of water molecules Bala subramanian (Fri Apr 03 2009 - 01:12:18 CDT)
- Re: [AMBER] How to find out residence time of water molecules Hannes Loeffler (Fri Apr 03 2009 - 02:31:32 CDT)
[AMBER] (no subject) chenquan (Fri Apr 03 2009 - 05:12:14 CDT)
- Re: [AMBER] (no subject) David A. Case (Fri Apr 03 2009 - 07:17:36 CDT)
[AMBER] How to create parameter file for unknown residue nicholus bhattacharjee (Fri Apr 03 2009 - 05:33:03 CDT)
- Re: [AMBER] How to create parameter file for unknown residue Marius Retegan (Fri Apr 03 2009 - 05:50:30 CDT)
[AMBER] Could not find angle parameter chenquan (Fri Apr 03 2009 - 05:46:47 CDT)
- Re: [AMBER] Could not find angle parameter Marius Retegan (Fri Apr 03 2009 - 05:58:47 CDT)
[AMBER] antechamber & multiple low-energy conformations Alessandro Nascimento (Fri Apr 03 2009 - 07:01:39 CDT)
[AMBER] amber9 serial compilation issues Francesco Pietra (Fri Apr 03 2009 - 13:38:12 CDT)
- Re: [AMBER] amber9 serial compilation issues David A. Case (Fri Apr 03 2009 - 15:01:02 CDT)
  - Re: [AMBER] amber9 serial compilation issues Francesco Pietra (Fri Apr 03 2009 - 17:04:17 CDT)
[AMBER] NALA-ALA-CALA peptide with antechamber Alan (Fri Apr 03 2009 - 11:33:17 CDT)
- Re: [AMBER] NALA-ALA-CALA peptide with antechamber David A. Case (Sat Apr 04 2009 - 08:04:32 CDT)
[AMBER] ptraj problem Ed Pate (Fri Apr 03 2009 - 15:13:37 CDT)
- Re: [AMBER] ptraj problem Thomas Cheatham III (Fri Apr 03 2009 - 15:23:21 CDT)
[AMBER] Generate AM1-CM2 charges using antechamber Sishi Tang (Fri Apr 03 2009 - 17:36:46 CDT)
[AMBER] parameter for amoeba Hemant Kumar (Sat Apr 04 2009 - 06:46:01 CDT)
[AMBER] LYN again Marius Retegan (Sat Apr 04 2009 - 08:12:09 CDT)
- Re: [AMBER] LYN again FyD (Sun Apr 05 2009 - 14:24:27 CDT)
  - Re: [AMBER] LYN again Marius Retegan (Mon Apr 06 2009 - 08:55:24 CDT)
    - Re: [AMBER] LYN again FyD (Mon Apr 06 2009 - 09:26:14 CDT)
[AMBER] deffision Nancy (Sat Apr 04 2009 - 09:30:50 CDT)
[AMBER] error in MM PBSA Vikas Sharma (Sat Apr 04 2009 - 12:06:57 CDT)
- Re: [AMBER] error in MM PBSA Hemant Gangwar (Sat Apr 04 2009 - 12:08:08 CDT)
- Re: [AMBER] error in MM PBSA David A. Case (Sat Apr 04 2009 - 16:16:42 CDT)
[AMBER] error in MM PBSA Vikas Sharma (Sun Apr 05 2009 - 01:09:35 CDT)
[AMBER] error in MM PBSA Vikas Sharma (Sun Apr 05 2009 - 23:27:21 CDT)
[AMBER] pmemd compilation/make failed - mkl_vml_service_threader_z_1i_c_1o Vijay Manickam Achari (Mon Apr 06 2009 - 02:27:24 CDT)
- Re: [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o Robert Duke (Mon Apr 06 2009 - 09:25:14 CDT)
  - Re: [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o Vijay Manickam Achari (Mon Apr 06 2009 - 23:25:36 CDT)
[AMBER] sander.MPI parallel run problem Dechang Li (Mon Apr 06 2009 - 02:44:12 CDT)
- Re: [AMBER] sander.MPI parallel run problem Carlos Simmerling (Mon Apr 06 2009 - 05:09:11 CDT)
  - Re: Re: [AMBER] sander.MPI parallel run problem Dechang Li (Mon Apr 06 2009 - 05:56:53 CDT)
    - Re: Re: [AMBER] sander.MPI parallel run problem Carlos Simmerling (Mon Apr 06 2009 - 06:02:13 CDT)
    - Re: Re: Re: [AMBER] sander.MPI parallel run problem Dechang Li (Mon Apr 06 2009 - 06:09:04 CDT)
[AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. Soni Mufaddal Saifee (Mon Apr 06 2009 - 04:07:51 CDT)
- Re: [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. Carlos Simmerling (Mon Apr 06 2009 - 05:07:09 CDT)
  - Re: [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. Soni Mufaddal Saifee (Tue Apr 07 2009 - 23:19:25 CDT)
[AMBER] MM-PBSA error while running heat.in Vikas Sharma (Mon Apr 06 2009 - 04:32:55 CDT)
[AMBER] ssh and make test.parallel Francesco Pietra (Mon Apr 06 2009 - 04:58:39 CDT)
- Re: [AMBER] ssh and make test.parallel Atro Tossavainen (Mon Apr 06 2009 - 05:33:21 CDT)
  - Re: [AMBER] ssh and make test.parallel Francesco Pietra (Mon Apr 06 2009 - 09:29:19 CDT)
[AMBER] problem with secstruct action command in ptraj nicholus bhattacharjee (Mon Apr 06 2009 - 06:49:44 CDT)
[AMBER] testing RRR with antechamber Alan (Mon Apr 06 2009 - 07:10:27 CDT)
[AMBER] zwitterionic form of ARG and antechamber Alan (Mon Apr 06 2009 - 07:33:31 CDT)
[AMBER] Amber with AMOEBA force-field Tomasio, Susana (Mon Apr 06 2009 - 07:41:18 CDT)
- Re: [AMBER] Amber with AMOEBA force-field David A. Case (Mon Apr 06 2009 - 07:47:11 CDT)
  - RE: [AMBER] Amber with AMOEBA force-field Tomasio, Susana (Mon Apr 06 2009 - 07:49:28 CDT)
    - Re: [AMBER] Amber with AMOEBA force-field Wei Zhang (Mon Apr 06 2009 - 07:55:59 CDT)
- Re: [AMBER] Amber with AMOEBA force-field Wei Zhang (Mon Apr 06 2009 - 07:48:28 CDT)
  - RE: [AMBER] Amber with AMOEBA force-field Tomasio, Susana (Mon Apr 06 2009 - 07:52:01 CDT)
[AMBER] Sander waleed_zalloum_at_yahoo.com (Mon Apr 06 2009 - 08:17:34 CDT)
[AMBER] MM-PBSA: decompose energy error Lucilla Angeli (Mon Apr 06 2009 - 09:35:58 CDT)
- Re: [AMBER] MM-PBSA: decompose energy error Maria Mirza (Sun Aug 16 2009 - 14:49:06 CDT)
[AMBER] Sander Stalling Steve Seibold (Mon Apr 06 2009 - 11:21:51 CDT)
- Re: [AMBER] Sander Stalling Robert Duke (Mon Apr 06 2009 - 11:57:18 CDT)
- RE: [AMBER] Sander Stalling Ross Walker (Mon Apr 06 2009 - 11:58:58 CDT)
- [AMBER] sequence function taufik.alsarraj_at_utoronto.ca (Mon Apr 06 2009 - 12:03:20 CDT)
  - Re: [AMBER] sequence function taufik.alsarraj_at_utoronto.ca (Mon Apr 06 2009 - 12:06:50 CDT)
[AMBER] Do I need to modify the cap residues nicholus bhattacharjee (Mon Apr 06 2009 - 11:45:20 CDT)
- RE: [AMBER] Do I need to modify the cap residues Ross Walker (Mon Apr 06 2009 - 12:00:05 CDT)
  - Re: [AMBER] Do I need to modify the cap residues nicholus bhattacharjee (Mon Apr 06 2009 - 12:19:41 CDT)
[AMBER] Negative "number of measurements" in PTRAJ Jenny Iskrenova (Mon Apr 06 2009 - 12:28:59 CDT)
- Re: [AMBER] Negative "number of measurements" in PTRAJ Thomas Cheatham (Tue Apr 07 2009 - 11:57:28 CDT)
[AMBER] Amber on GPU Sasha Buzko (Mon Apr 06 2009 - 19:56:31 CDT)
- RE: [AMBER] Amber on GPU Ross Walker (Mon Apr 06 2009 - 20:14:07 CDT)
[AMBER] deffision coefficient Nancy (Mon Apr 06 2009 - 20:18:32 CDT)
- Re: [AMBER] deffision coefficient David A. Case (Mon Apr 06 2009 - 21:16:39 CDT)
[AMBER] A question about SMD force constant Jackie. J. Shen (Mon Apr 06 2009 - 20:40:13 CDT)
- Re: [AMBER] A question about SMD force constant Carlos Simmerling (Tue Apr 07 2009 - 05:32:09 CDT)
[AMBER] ambmask question Ed Pate (Mon Apr 06 2009 - 23:36:40 CDT)
[AMBER] Problems with running two separate jobs in the same time Antonija TomiÄ‡ (Tue Apr 07 2009 - 03:08:53 CDT)
- RE: [AMBER] Problems with running two separate jobs in the same time Ross Walker (Tue Apr 07 2009 - 10:01:14 CDT)
  - RE: [AMBER] Problems with running two separate jobs in the same time Antonija TomiÄ‡ (Thu Apr 09 2009 - 05:33:03 CDT)
[AMBER] how to add charge in metal ion bharat lakhani (Tue Apr 07 2009 - 04:11:23 CDT)
- RE: [AMBER] how to add charge in metal ion Ross Walker (Tue Apr 07 2009 - 10:01:14 CDT)
  - Re: [AMBER] how to add charge in metal ion bharat lakhani (Tue Apr 14 2009 - 07:49:44 CDT)
[AMBER] missing violations of the covalent geometry Helena P M Tossavainen (Tue Apr 07 2009 - 04:36:44 CDT)
- Re: [AMBER] missing violations of the covalent geometry David A. Case (Tue Apr 07 2009 - 06:10:42 CDT)
  - Re: [AMBER] missing violations of the covalent geometry Helena P M Tossavainen (Tue Apr 07 2009 - 07:10:16 CDT)
[AMBER] errors while testing Per Jr. Greisen (Tue Apr 07 2009 - 05:00:19 CDT)
- Re: [AMBER] errors while testing Atro Tossavainen (Tue Apr 07 2009 - 05:18:08 CDT)
  - Re: [AMBER] errors while testing Per Jr. Greisen (Wed Apr 08 2009 - 06:06:40 CDT)
[AMBER] Problem with CAP residues Tomasio, Susana (Tue Apr 07 2009 - 05:17:27 CDT)
- Re: [AMBER] Problem with CAP residues FyD (Tue Apr 07 2009 - 06:01:35 CDT)
[AMBER] TI production runs stop after a certain Step number Hannes Wallnoefer (Tue Apr 07 2009 - 06:48:45 CDT)
- Re: [AMBER] TI production runs stop after a certain Step number steinbrt_at_rci.rutgers.edu (Tue Apr 07 2009 - 09:49:57 CDT)
  - Re: [AMBER] TI production runs stop after a certain Step number Hannes Wallnoefer (Wed Apr 08 2009 - 06:48:31 CDT)
    - Re: [AMBER] TI production runs stop after a certain Step number steinbrt_at_rci.rutgers.edu (Wed Apr 08 2009 - 09:35:11 CDT)
    - Re: [AMBER] TI production runs stop after a certain Step number Hannes Wallnoefer (Wed Apr 08 2009 - 10:14:32 CDT)
- Re: [AMBER] TI production runs stop after a certain Step number Ilyas Yildirim (Tue Apr 07 2009 - 14:08:31 CDT)
[AMBER] problem in calculation of binding energy in final step (MM-PBSA) Maryam Hamzehee (Tue Apr 07 2009 - 08:59:03 CDT)
[AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana (Tue Apr 07 2009 - 10:16:08 CDT)
- Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error David A. Case (Tue Apr 07 2009 - 11:29:18 CDT)
  - RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana (Tue Apr 07 2009 - 11:34:57 CDT)
[AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra (Tue Apr 07 2009 - 13:56:25 CDT)
- [AMBER] prmtop residue format taufik.alsarraj_at_utoronto.ca (Tue Apr 07 2009 - 15:04:25 CDT)
  - Re: [AMBER] prmtop residue format David A. Case (Tue Apr 07 2009 - 15:35:40 CDT)
    - Re: [AMBER] top2mol2 taufik.alsarraj_at_utoronto.ca (Tue Apr 07 2009 - 17:39:34 CDT)
    - [AMBER] ptraj randomizeions taufik.alsarraj_at_utoronto.ca (Tue Apr 07 2009 - 18:32:23 CDT)
- Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen (Wed Apr 08 2009 - 04:35:17 CDT)
  - Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra (Wed Apr 08 2009 - 05:03:09 CDT)
[AMBER] PBSA Radii option quantum_mania_at_yahoo.com (Tue Apr 07 2009 - 14:31:18 CDT)
- [AMBER] Source of new CYX residue parameters in ff03ua Chris Moth (Tue Apr 07 2009 - 14:48:46 CDT)
  - [AMBER] Source of new CYX residue parameters in ff03ua Chris Moth (Tue Apr 14 2009 - 19:42:33 CDT)
    - RE: [AMBER] Source of new CYX residue parameters in ff03ua Ross Walker (Tue Apr 14 2009 - 23:08:14 CDT)
[AMBER] MMPB(GB)SA on trimer quantum_mania_at_yahoo.com (Tue Apr 07 2009 - 20:01:39 CDT)
[AMBER] compare MMPBSA result m m (Wed Apr 08 2009 - 01:28:06 CDT)
- RE: [AMBER] compare MMPBSA result Ray Luo (Wed Apr 08 2009 - 12:02:41 CDT)
[AMBER] problem with antechamber aneesh cna (Wed Apr 08 2009 - 01:32:32 CDT)
[AMBER] please help me out bharat lakhani (Wed Apr 08 2009 - 04:18:41 CDT)
- RE: [AMBER] please help me out Ross Walker (Wed Apr 08 2009 - 10:34:51 CDT)
  - Re: [AMBER] please help me out Hugh Heldenbrand (Wed Apr 08 2009 - 10:44:54 CDT)
    - Re: [AMBER] please help me out David A. Case (Wed Apr 08 2009 - 13:10:04 CDT)
  - [AMBER] ntwr taufik.alsarraj_at_utoronto.ca (Wed Apr 08 2009 - 16:45:01 CDT)
[AMBER] Failures of tests Per Jr. Greisen (Wed Apr 08 2009 - 10:41:34 CDT)
- RE: [AMBER] Failures of tests Seetin, Matthew (Wed Apr 08 2009 - 10:57:27 CDT)
  - Re: [AMBER] Failures of tests Per Jr. Greisen (Wed Apr 08 2009 - 11:17:16 CDT)
- Re: [AMBER] Failures of tests Atro Tossavainen (Wed Apr 08 2009 - 17:43:08 CDT)
  - Re: [AMBER] Failures of tests Per Jr. Greisen (Thu Apr 09 2009 - 07:52:32 CDT)
[AMBER] Thermodynamic Integration and belly Ignacio J. General (Wed Apr 08 2009 - 14:52:51 CDT)
[AMBER] force fields Mark M Huntress (Wed Apr 08 2009 - 19:23:38 CDT)
- RE: [AMBER] force fields Ross Walker (Wed Apr 08 2009 - 19:36:05 CDT)
- Re: [AMBER] force fields Gustavo Seabra (Wed Apr 15 2009 - 07:43:49 CDT)
[AMBER] please help me out bharat lakhani (Thu Apr 09 2009 - 00:10:22 CDT)
- Re: [AMBER] please help me out David A. Case (Thu Apr 09 2009 - 06:46:12 CDT)
[AMBER] how to plot this kind of map? lnin_1431_at_sina.com (Thu Apr 09 2009 - 03:36:45 CDT)
- Re: [AMBER] how to plot this kind of map? Dechang Li (Thu Apr 09 2009 - 03:46:16 CDT)
[AMBER] hpux sander.serial failure info Yiannis Georgiadis (Thu Apr 09 2009 - 17:28:28 CDT)
- Re: [AMBER] hpux sander.serial failure info David A. Case (Thu Apr 09 2009 - 06:56:51 CDT)
  - Re: [AMBER] hpux sander.serial failure info Yiannis Georgiadis (Wed Apr 15 2009 - 16:41:06 CDT)
    - Re: [AMBER] hpux sander.serial failure info David A. Case (Wed Apr 15 2009 - 07:07:45 CDT)
[AMBER] RST file waleed zalloum (Thu Apr 09 2009 - 09:06:37 CDT)
- Re: [AMBER] RST file David A. Case (Fri Apr 10 2009 - 07:21:19 CDT)
[AMBER] Release of R.E.D. Server FyD (Thu Apr 09 2009 - 03:31:30 CDT)
[AMBER] antechamber problems Jia Xu (Thu Apr 09 2009 - 12:12:44 CDT)
- Re: [AMBER] antechamber problems David A. Case (Thu Apr 09 2009 - 13:04:51 CDT)
- Re: [AMBER] antechamber problems Nicholas Musolino (Thu Apr 09 2009 - 13:03:45 CDT)
  - Re: [AMBER] antechamber problems Jia Xu (Fri Apr 10 2009 - 09:41:53 CDT)
[AMBER] Sander and multiple residues Dan Kaps (Thu Apr 09 2009 - 13:48:55 CDT)
- Re: [AMBER] Sander and multiple residues Carlos Simmerling (Thu Apr 09 2009 - 14:21:56 CDT)
  - Re: [AMBER] Sander and multiple residues Dan Kaps (Thu Apr 09 2009 - 15:02:46 CDT)
    - Re: [AMBER] Sander and multiple residues Carlos Simmerling (Thu Apr 09 2009 - 15:05:23 CDT)
    - Re: [AMBER] Sander and multiple residues Dan Kaps (Fri Apr 10 2009 - 07:56:53 CDT)
- Re: [AMBER] Sander and multiple residues Bill Ross (Thu Apr 09 2009 - 15:12:10 CDT)
  - Re: [AMBER] Sander and multiple residues Dan Kaps (Fri Apr 10 2009 - 07:57:54 CDT)
    - Re: [AMBER] Sander and multiple residues David A. Case (Fri Apr 10 2009 - 09:03:57 CDT)
    - Re: [AMBER] Sander and multiple residues Dan Kaps (Fri Apr 10 2009 - 10:01:08 CDT)
- Re: [AMBER] Sander and multiple residues Bill Ross (Fri Apr 10 2009 - 11:42:36 CDT)
  - Re: [AMBER] Sander and multiple residues Dan Kaps (Fri Apr 10 2009 - 12:46:49 CDT)
  - [AMBER] ptraj (vector and corrplane) taufik.alsarraj_at_utoronto.ca (Fri Apr 10 2009 - 19:45:46 CDT)
- Re: [AMBER] Sander and multiple residues Bill Ross (Fri Apr 10 2009 - 15:42:14 CDT)
[AMBER] igb=0 vs. igb=6 give different answers Hugh Heldenbrand (Thu Apr 09 2009 - 15:51:02 CDT)
- Re: [AMBER] igb=0 vs. igb=6 give different answers David A. Case (Thu Apr 09 2009 - 21:48:31 CDT)
[AMBER] basepair balaji nagarajan (Fri Apr 10 2009 - 00:30:57 CDT)
- Re: [AMBER] basepair Bala subramanian (Tue Apr 14 2009 - 06:09:21 CDT)
[AMBER] Amber 1.2 tools test suite failure? Jim Parker (Sat Apr 11 2009 - 12:41:54 CDT)
- RE: [AMBER] Amber 1.2 tools test suite failure? Ross Walker (Sat Apr 11 2009 - 13:00:45 CDT)
  - Re: [AMBER] Solved-Amber 1.2 tools test suite failure Jim Parker (Sat Apr 11 2009 - 14:29:55 CDT)
    - RE: [AMBER] Solved-Amber 1.2 tools test suite failure Ross Walker (Sat Apr 11 2009 - 14:51:13 CDT)
[AMBER] install and test Amber 10 parallel on Ubuntu 8.10 Jim Parker (Sat Apr 11 2009 - 19:20:25 CDT)
- [AMBER] Re: install and test Amber 10 parallel on Ubuntu 8.10 Jim Parker (Sat Apr 11 2009 - 23:47:19 CDT)
[AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm Alan (Sun Apr 12 2009 - 04:30:15 CDT)
- Re: [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm Wei Zhang (Sun Apr 12 2009 - 08:24:47 CDT)
  - Re: [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm Alan (Sun Apr 12 2009 - 10:58:18 CDT)
[AMBER] problem with explicit solvent in TMD balaji nagarajan (Mon Apr 13 2009 - 06:37:21 CDT)
- Re: [AMBER] problem with explicit solvent in TMD Carlos Simmerling (Mon Apr 13 2009 - 06:41:41 CDT)
- RE: [AMBER] problem with explicit solvent in TMD Ross Walker (Mon Apr 13 2009 - 10:29:11 CDT)
[AMBER] Energy minimisation and NaN vivek.viv.sharma_at_gmail.com (Mon Apr 13 2009 - 06:55:55 CDT)
- Re: [AMBER] Energy minimisation and NaN David A. Case (Mon Apr 13 2009 - 14:28:10 CDT)
[AMBER] atom types in pdb files Dan Kaps (Mon Apr 13 2009 - 09:23:58 CDT)
- RE: [AMBER] atom types in pdb files Kristina Furse (Mon Apr 13 2009 - 11:30:05 CDT)
  - Re: [AMBER] atom types in pdb files Dan Kaps (Mon Apr 13 2009 - 14:29:43 CDT)
    - Re: [AMBER] atom types in pdb files David A. Case (Mon Apr 13 2009 - 15:25:04 CDT)
[AMBER] Thermodynamic Integration and belly Ignacio J. General (Mon Apr 13 2009 - 10:24:15 CDT)
- Re: [AMBER] Thermodynamic Integration and belly steinbrt_at_rci.rutgers.edu (Mon Apr 13 2009 - 11:46:19 CDT)
  - Re: [AMBER] Thermodynamic Integration and belly Ignacio J. General (Mon Apr 13 2009 - 12:26:16 CDT)
[AMBER] error saving prmtop and inpcrd files of complex in MM-PBSA Vikas Sharma (Mon Apr 13 2009 - 15:11:07 CDT)
[AMBER] restrained minimization quantum_mania_at_yahoo.com (Mon Apr 13 2009 - 19:12:35 CDT)
- Re: [AMBER] restrained minimization David A. Case (Mon Apr 13 2009 - 21:03:11 CDT)
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Marek Malý (Mon Apr 13 2009 - 22:29:17 CDT)
- RE: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Ross Walker (Mon Apr 13 2009 - 23:10:38 CDT)
  - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Marek Malý (Tue Apr 14 2009 - 18:18:18 CDT)
[AMBER] chosing complex in amber Vikas Sharma (Tue Apr 14 2009 - 00:18:43 CDT)
[AMBER] Questions on targeted MD with explicit solvent Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Tue Apr 14 2009 - 08:51:40 CDT)
[AMBER] [qm/mm] qmcharge for acidic a.a. in proteins sychen (Tue Apr 14 2009 - 11:33:03 CDT)
- RE: [AMBER] [qm/mm] qmcharge for acidic a.a. in proteins Ross Walker (Tue Apr 14 2009 - 14:45:06 CDT)
[AMBER] antechamber and wrong net charge with gasteiger method Alan (Tue Apr 14 2009 - 12:41:30 CDT)
- Re: [AMBER] antechamber and wrong net charge with gasteiger method David A. Case (Tue Apr 14 2009 - 13:42:14 CDT)
[AMBER] my FF m m (Tue Apr 14 2009 - 17:21:38 CDT)
- Re: [AMBER] my FF David A. Case (Wed Apr 15 2009 - 07:28:16 CDT)
[AMBER] water bonding with protein Mark M Huntress (Tue Apr 14 2009 - 21:55:39 CDT)
- Re: [AMBER] water bonding with protein David A. Case (Wed Apr 15 2009 - 06:58:17 CDT)
[AMBER] hbond_ptraj_eror balaji nagarajan (Wed Apr 15 2009 - 01:53:29 CDT)
[AMBER] mean of character in frcmod.ff03 chenquan (Wed Apr 15 2009 - 07:26:38 CDT)
- RE: [AMBER] mean of character in frcmod.ff03 Ross Walker (Wed Apr 15 2009 - 09:58:31 CDT)
  - RE: [AMBER] mean of character in frcmod.ff03 chenquan (Wed Apr 15 2009 - 18:36:32 CDT)
[AMBER] help- regarding - TMD balaji nagarajan (Wed Apr 15 2009 - 11:19:59 CDT)
- RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Wed Apr 15 2009 - 12:56:07 CDT)
  - RE: [AMBER] help- regarding - TMD balaji nagarajan (Thu Apr 16 2009 - 00:21:26 CDT)
    - RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Thu Apr 16 2009 - 08:30:22 CDT)
    - RE: [AMBER] help- regarding - TMD balaji nagarajan (Thu Apr 16 2009 - 12:01:39 CDT)
- RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Mon Apr 20 2009 - 10:05:38 CDT)
  - Re: [AMBER] help- regarding - TMD Carlos Simmerling (Mon Apr 20 2009 - 10:12:40 CDT)
[AMBER] please help me out bharat lakhani (Thu Apr 16 2009 - 01:41:08 CDT)
[AMBER] missing amber force field parameters Neha Gandhi (Thu Apr 16 2009 - 04:19:57 CDT)
- Re: [AMBER] missing amber force field parameters FyD (Thu Apr 16 2009 - 04:41:44 CDT)
[AMBER] pmemd in amber10 - compile failed in HPC Vijay Manickam Achari (Thu Apr 16 2009 - 05:13:49 CDT)
- Re: [AMBER] pmemd in amber10 - compile failed in HPC Robert Duke (Thu Apr 16 2009 - 07:24:45 CDT)
[AMBER] 1-4 vdW, GB MM difference Jimmy Heimdal (Thu Apr 16 2009 - 06:57:01 CDT)
- Re: [AMBER] 1-4 vdW, GB MM difference David A. Case (Thu Apr 16 2009 - 09:47:55 CDT)
[AMBER] ambertools failed - SMP IA64 Vijay Manickam Achari (Thu Apr 16 2009 - 08:17:34 CDT)
- Re: [AMBER] ambertools failed - SMP IA64 David A. Case (Thu Apr 16 2009 - 09:10:20 CDT)
[AMBER] Van der Waals atom types Antonio Morreale (Thu Apr 16 2009 - 09:39:14 CDT)
[AMBER] Amber and CHARMM summer school David A. Case (Thu Apr 16 2009 - 10:04:18 CDT)
[AMBER] Bad value during integer read by sander Collins Nganou (Thu Apr 16 2009 - 10:09:45 CDT)
[AMBER] sulfonamide parameters valeria.lapietra_at_unina.it (Thu Apr 16 2009 - 10:16:49 CDT)
[AMBER] polarizable force field for 18-crown-6 Gert von Helden (Thu Apr 16 2009 - 12:33:15 CDT)
- Re: [AMBER] polarizable force field for 18-crown-6 Piotr Cieplak (Fri Apr 17 2009 - 02:48:03 CDT)
[AMBER] help regarding force fields Vikas Sharma (Fri Apr 17 2009 - 01:06:32 CDT)
[AMBER] Right force fields Vikas Sharma (Fri Apr 17 2009 - 01:22:16 CDT)
- Re: [AMBER] Right force fields Patrick Schopf (Fri Apr 17 2009 - 07:48:14 CDT)
  - Re: [AMBER] Right force fields Vikas Sharma (Fri Apr 17 2009 - 08:14:04 CDT)
    - Re: [AMBER] Right force fields Patrick Schopf (Fri Apr 17 2009 - 08:34:04 CDT)
[AMBER] radius of gyration Beale, John (Fri Apr 17 2009 - 06:39:31 CDT)
[AMBER] Density in MD simulation Ibrahim Moustafa (Fri Apr 17 2009 - 11:09:16 CDT)
- Re: [AMBER] Density in MD simulation Carlos Simmerling (Fri Apr 17 2009 - 11:10:51 CDT)
  - Re: [AMBER] Density in MD simulation Ibrahim Moustafa (Fri Apr 17 2009 - 18:26:46 CDT)
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? quantum_mania_at_yahoo.com (Fri Apr 17 2009 - 12:52:28 CDT)
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Lachele Foley (Lists) (Fri Apr 17 2009 - 13:13:49 CDT)
[AMBER] Backbone restraint Rilei Yu (Fri Apr 17 2009 - 21:30:38 CDT)
- Re: [AMBER] Backbone restraint Carlos Simmerling (Fri Apr 17 2009 - 21:35:26 CDT)
- Re: [AMBER] Backbone restraint Rilei Yu (Fri Apr 17 2009 - 22:29:12 CDT)
  - Re: [AMBER] Backbone restraint Carlos Simmerling (Sat Apr 18 2009 - 06:08:39 CDT)
    - Re: Re: [AMBER] Backbone restraint Rilei Yu (Mon Apr 20 2009 - 20:21:09 CDT)
  - Re: Re: [AMBER] Backbone restraint Jackie. J. Shen (Mon Apr 20 2009 - 20:12:13 CDT)
[AMBER] help_me to know the reason balaji nagarajan (Fri Apr 17 2009 - 23:30:07 CDT)
- Re: [AMBER] help_me to know the reason Carlos Simmerling (Sat Apr 18 2009 - 05:53:50 CDT)
[AMBER] please read this mail bharat lakhani (Sat Apr 18 2009 - 02:38:12 CDT)
- Re: [AMBER] please read this mail David A. Case (Sat Apr 18 2009 - 08:01:08 CDT)
[AMBER] about saltcon zgong.hust (Sat Apr 18 2009 - 21:45:53 CDT)
- Re: [AMBER] about saltcon Carlos Simmerling (Sun Apr 19 2009 - 05:49:57 CDT)
[AMBER] Atom type error Vikas Sharma (Sun Apr 19 2009 - 04:48:01 CDT)
- Re: [AMBER] Atom type error nicholus bhattacharjee (Sun Apr 19 2009 - 05:55:37 CDT)
  - Re: [AMBER] Atom type error Carlos Simmerling (Sun Apr 19 2009 - 06:06:07 CDT)
    - Re: [AMBER] Atom type error Vikas Sharma (Sun Apr 19 2009 - 11:49:53 CDT)
  - Re: [AMBER] Atom type error Vikas Sharma (Sun Apr 19 2009 - 11:50:28 CDT)
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý (Mon Apr 20 2009 - 06:52:36 CDT)
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Karl Kirschner (Mon Apr 20 2009 - 07:27:45 CDT)
  - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý (Mon Apr 20 2009 - 22:52:46 CDT)
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail FyD (Mon Apr 20 2009 - 09:50:12 CDT)
[AMBER] Partial interactions Ignacio J. General (Mon Apr 20 2009 - 16:07:24 CDT)
- Re: [AMBER] Partial interactions steinbrt_at_rci.rutgers.edu (Mon Apr 20 2009 - 16:47:35 CDT)
  - Re: [AMBER] Partial interactions Ignacio J. General (Tue Apr 21 2009 - 09:31:26 CDT)
[AMBER] My step size Vikas Sharma (Tue Apr 21 2009 - 01:50:16 CDT)
- RE: [AMBER] My step size Ross Walker (Tue Apr 21 2009 - 06:27:07 CDT)
  - Re: [AMBER] My step size Vikas Sharma (Tue Apr 21 2009 - 10:01:25 CDT)
  - Re: [AMBER] My step size Vikas Sharma (Tue Apr 21 2009 - 23:49:47 CDT)
[AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 06:12:27 CDT)
- Re: [AMBER] atom numbers David A. Case (Tue Apr 21 2009 - 06:54:37 CDT)
  - Re: [AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 10:33:12 CDT)
- Re: [AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 12:15:07 CDT)
- Re: [AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 13:36:35 CDT)
[AMBER] Number of LES copies in ptraj Thomas Exner (Tue Apr 21 2009 - 10:28:41 CDT)
[AMBER] Set start timestep for mdcrd traj output quantum_mania_at_yahoo.com (Tue Apr 21 2009 - 11:38:53 CDT)
- Re: [AMBER] Set start timestep for mdcrd traj output Carlos Simmerling (Tue Apr 21 2009 - 18:26:02 CDT)
  - Re: [AMBER] Set start timestep for mdcrd traj output Dong Xu (Tue Apr 21 2009 - 18:44:50 CDT)
[AMBER] Set start timestep for mdcrd traj output quantum_mania_at_yahoo.com (Tue Apr 21 2009 - 11:31:45 CDT)
[AMBER] Flexible ring simulation Dong Xu (Tue Apr 21 2009 - 18:04:55 CDT)
[AMBER] per atom energies in sander/pmemd Tamara Rogers (Tue Apr 21 2009 - 18:41:27 CDT)
[AMBER] Disulfide bond Dong Xu (Tue Apr 21 2009 - 20:37:46 CDT)
- Re: [AMBER] Disulfide bond Wei Zhang (Tue Apr 21 2009 - 20:46:19 CDT)
  - Re: [AMBER] Disulfide bond Dong Xu (Tue Apr 21 2009 - 21:41:02 CDT)
[AMBER] bintraj and amber 10 Naser Alijabbari (Wed Apr 22 2009 - 01:31:51 CDT)
- RE: [AMBER] bintraj and amber 10 Ross Walker (Wed Apr 22 2009 - 05:59:47 CDT)
  - Re: [AMBER] bintraj and amber 10 Naser Alijabbari (Wed Apr 22 2009 - 20:05:21 CDT)
[AMBER] help regarding step size Vikas Sharma (Wed Apr 22 2009 - 03:57:31 CDT)
- Re: [AMBER] help regarding step size Carlos Simmerling (Wed Apr 22 2009 - 05:13:54 CDT)
  - Re: [AMBER] help regarding step size Vikas Sharma (Wed Apr 22 2009 - 05:50:27 CDT)
    - Re: [AMBER] help regarding step size Carlos Simmerling (Wed Apr 22 2009 - 06:03:28 CDT)
    - Re: [AMBER] help regarding step size Vikas Sharma (Wed Apr 22 2009 - 23:40:33 CDT)
[AMBER] uncharged c and n terminal amino acids Christopher Materese (Wed Apr 22 2009 - 13:05:38 CDT)
- Re: [AMBER] uncharged c and n terminal amino acids David A. Case (Wed Apr 22 2009 - 13:16:19 CDT)
[AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Wed Apr 22 2009 - 16:55:58 CDT)
- RE: [AMBER] Problem with RNA hairpin unwinding in explicit water Seetin, Matthew (Wed Apr 22 2009 - 17:22:29 CDT)
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Carlos Simmerling (Wed Apr 22 2009 - 17:25:47 CDT)
  - Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Wed Apr 22 2009 - 17:34:35 CDT)
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Thomas Cheatham III (Wed Apr 22 2009 - 17:56:25 CDT)
  - Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Wed Apr 22 2009 - 18:10:55 CDT)
[AMBER] Amber Sulfate Ion Parameters Gary Clark (Wed Apr 22 2009 - 17:31:00 CDT)
- Re: [AMBER] Amber Sulfate Ion Parameters FyD (Thu Apr 23 2009 - 00:18:28 CDT)
- Re: [AMBER] Amber Sulfate Ion Parameters FyD (Thu Apr 23 2009 - 01:07:40 CDT)
  - Re: [AMBER] Amber Sulfate Ion Parameters Gary Clark (Thu Apr 23 2009 - 14:55:24 CDT)
[AMBER] error in output file Vikas Sharma (Thu Apr 23 2009 - 06:39:42 CDT)
- Re: [AMBER] error in output file Carlos Simmerling (Thu Apr 23 2009 - 06:42:02 CDT)
  - Re: [AMBER] error in output file Vikas Sharma (Thu Apr 23 2009 - 06:58:24 CDT)
[AMBER] nmod no run proprely in mmbsa mohamed mohamed (Thu Apr 23 2009 - 07:20:36 CDT)
- Re: [AMBER] nmod no run proprely in mmbsa David A. Case (Thu Apr 23 2009 - 07:47:44 CDT)
[AMBER] Regarding syntax for freezing different atoms Jorgen Simonsen (Thu Apr 23 2009 - 07:50:43 CDT)
- RE: [AMBER] Regarding syntax for freezing different atoms Ross Walker (Thu Apr 23 2009 - 08:24:55 CDT)
[AMBER] Amber Installation problem ÁÖÅÂ¼º (Thu Apr 23 2009 - 08:10:42 CDT)
- RE: [AMBER] Amber Installation problem Ross Walker (Thu Apr 23 2009 - 08:16:18 CDT)
[AMBER] NAB bug with parmbsc0 David A. Case (Thu Apr 23 2009 - 11:25:27 CDT)
Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Bill Ross (Thu Apr 23 2009 - 12:53:40 CDT)
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Thu Apr 23 2009 - 12:55:58 CDT)
[AMBER] Unit name with loadMol2 command Nicholas Musolino (Thu Apr 23 2009 - 14:30:30 CDT)
- Re: [AMBER] Unit name with loadMol2 command David A. Case (Thu Apr 23 2009 - 17:54:02 CDT)
[AMBER] CY3 dye parameters jcmoore_at_student.umass.edu (Thu Apr 23 2009 - 16:42:59 CDT)
- Re: [AMBER] CY3 dye parameters FyD (Sat Apr 25 2009 - 01:04:22 CDT)
- Re: [AMBER] CY3 dye parameters Brent Krueger (Sat Apr 25 2009 - 14:33:40 CDT)
[AMBER] Amber Installation problem ÁÖÅÂ¼º (Thu Apr 23 2009 - 20:35:46 CDT)
[AMBER] Equilibrium bond lengths and angle values Dmitri Nilov (Fri Apr 24 2009 - 08:19:56 CDT)
- Re: [AMBER] Equilibrium bond lengths and angle values FyD (Fri Apr 24 2009 - 16:05:42 CDT)
  - Re: [AMBER] Equilibrium bond lengths and angle values Dmitri Nilov (Tue Apr 28 2009 - 05:56:38 CDT)
[AMBER] Simulated annealing waleed zalloum (Fri Apr 24 2009 - 09:31:36 CDT)
- Re: [AMBER] Simulated annealing Carlos Simmerling (Fri Apr 24 2009 - 09:49:40 CDT)
[AMBER] question Tatyana Fedotova (Fri Apr 24 2009 - 14:55:40 CDT)
[AMBER] restraint constant Dong Xu (Sat Apr 25 2009 - 17:15:22 CDT)
[AMBER] Papers on Amber package usage Andrew Voronkov (Sun Apr 26 2009 - 00:07:42 CDT)
- Re: [AMBER] Papers on Amber package usage David A. Case (Sun Apr 26 2009 - 07:48:31 CDT)
[AMBER] amber question Vikas Sharma (Sun Apr 26 2009 - 01:00:06 CDT)
- Re: [AMBER] amber question Barbault Florent (Sun Apr 26 2009 - 03:48:31 CDT)
  - Re: [AMBER] amber question Vikas Sharma (Sun Apr 26 2009 - 04:51:38 CDT)
  - Re: [AMBER] amber question Vikas Sharma (Sun Apr 26 2009 - 04:56:26 CDT)
[AMBER] Water-molecules sikander azam (Sun Apr 26 2009 - 08:11:33 CDT)
- Re: [AMBER] Water-molecules case (Sun Apr 26 2009 - 17:35:36 CDT)
  - [AMBER] MM-GBSA Free enegy decomposition Rajesh Raju (Mon Apr 27 2009 - 07:27:23 CDT)
[AMBER] Install ÁÖÅÂ¼º (Sun Apr 26 2009 - 08:45:45 CDT)
[AMBER] Using smd with fixed atom nandy_at_physics.iisc.ernet.in (Sun Apr 26 2009 - 09:57:45 CDT)
[AMBER] AmberTools compiling error Farly Walsh (Sun Apr 26 2009 - 19:40:38 CDT)
- RE: [AMBER] AmberTools compiling error Ross Walker (Sun Apr 26 2009 - 20:55:06 CDT)
  - Re: [AMBER] AmberTools compiling error Farly Walsh (Wed Apr 29 2009 - 14:49:27 CDT)
[AMBER] Error with calculation of the potential energy Per Jr. Greisen (Mon Apr 27 2009 - 06:03:44 CDT)
- Re: [AMBER] Error with calculation of the potential energy Carlos Simmerling (Mon Apr 27 2009 - 06:08:47 CDT)
  - Re: [AMBER] Error with calculation of the potential energy Per Jr. Greisen (Mon Apr 27 2009 - 12:11:32 CDT)
[AMBER] Mixing of forcefields in case of covaletly bonded systems Marek Malý (Mon Apr 27 2009 - 07:06:38 CDT)
[AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing Tommaso Cupido (Mon Apr 27 2009 - 09:10:12 CDT)
- Re: [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing David A. Case (Mon Apr 27 2009 - 12:30:55 CDT)
  - Re: [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing Piotr Cieplak (Mon Apr 27 2009 - 14:07:38 CDT)
  - [AMBER] ERROR In Restraint file. Catein Catherine (Tue Apr 28 2009 - 10:12:34 CDT)
[AMBER] pmemd compilation error john smith (Mon Apr 27 2009 - 22:30:21 CDT)
- Re: [AMBER] pmemd compilation error Robert Duke (Mon Apr 27 2009 - 23:09:15 CDT)
  - Re: [AMBER] pmemd compilation error john smith (Tue May 05 2009 - 06:20:08 CDT)
[AMBER] Best rms fit for correlation and covariance analysis Cihan Aydin (Tue Apr 28 2009 - 00:02:14 CDT)
[AMBER] dipole autocorrelation functions aneesh cna (Tue Apr 28 2009 - 01:23:05 CDT)
Fwd: [AMBER] MM-GBSA Free enegy decomposition Rajesh Raju (Tue Apr 28 2009 - 06:28:17 CDT)
[AMBER] transport properties oguz gurbulak (Tue Apr 28 2009 - 09:11:05 CDT)
[AMBER] reg-TMD balaji nagarajan (Tue Apr 28 2009 - 10:23:34 CDT)
- Re: [AMBER] reg-TMD Carlos Simmerling (Tue Apr 28 2009 - 12:48:18 CDT)
  - RE: [AMBER] reg-TMD balaji nagarajan (Tue Apr 28 2009 - 23:16:17 CDT)
Re: [AMBER] Best rms fit for correlation and covariance analysis Bill Ross (Tue Apr 28 2009 - 11:57:10 CDT)
[AMBER] Restraining counterions? Francesco Pietra (Tue Apr 28 2009 - 12:32:18 CDT)
Re: [AMBER] Restraining counterions? Bill Ross (Tue Apr 28 2009 - 13:59:52 CDT)
[AMBER] ANAL problems E.M. (Tue Apr 28 2009 - 15:12:04 CDT)
Re: [AMBER] ANAL problems Bill Ross (Tue Apr 28 2009 - 15:40:59 CDT)
- Re: [AMBER] ANAL problems Edward M (Tue Apr 28 2009 - 18:01:34 CDT)
[AMBER] Using AMBER force fields in NAMD Michael Zimmermann (Tue Apr 28 2009 - 16:25:56 CDT)
- RE: [AMBER] Using AMBER force fields in NAMD Ross Walker (Tue Apr 28 2009 - 17:17:06 CDT)
  - RE: [AMBER] Using AMBER force fields in NAMD Piotr Cieplak (Tue Apr 28 2009 - 17:23:15 CDT)
  - RE: [AMBER] Using AMBER force fields in NAMD Thomas Cheatham III (Tue Apr 28 2009 - 17:45:15 CDT)
[AMBER] parallel problem of QM/MM calculation for AMBER 9 liu junjun (Tue Apr 28 2009 - 16:53:06 CDT)
- RE: [AMBER] parallel problem of QM/MM calculation for AMBER 9 Ross Walker (Tue Apr 28 2009 - 17:24:12 CDT)
  - Re: [AMBER] parallel problem of QM/MM calculation for AMBER 9 liu junjun (Tue Apr 28 2009 - 21:18:31 CDT)
[AMBER] The PDB file was not recognized by Amber, what can i do? Houyang Chen (Tue Apr 28 2009 - 17:00:05 CDT)
- Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Carlos Simmerling (Tue Apr 28 2009 - 17:03:57 CDT)
- Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Barbault Florent (Tue Apr 28 2009 - 18:00:55 CDT)
  - RE: [AMBER] The PDB file was not recognized by Amber, what can i do? Houyang Chen (Tue Apr 28 2009 - 22:42:39 CDT)
    - RE: [AMBER] The PDB file was not recognized by Amber, what can i do? Ross Walker (Tue Apr 28 2009 - 22:56:27 CDT)
    - Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Barbault Florent (Wed Apr 29 2009 - 01:56:09 CDT)
- Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Markus Kaukonen (Wed Apr 29 2009 - 02:16:30 CDT)
  - RE: [AMBER] The PDB file was not recognized by Amber, what can i do? Houyang Chen (Wed Apr 29 2009 - 17:17:51 CDT)
[AMBER] Nonterminal, was not found in name map Sunita Patel (Tue Apr 28 2009 - 19:50:08 CDT)
- RE: [AMBER] Nonterminal, was not found in name map Ross Walker (Tue Apr 28 2009 - 21:49:50 CDT)
- RE: [AMBER] Nonterminal, was not found in name map Bill Ross (Wed Apr 29 2009 - 00:05:12 CDT)
[AMBER] REd program! R. A. (Tue Apr 28 2009 - 23:37:38 CDT)
- Re: [AMBER] REd program! FyD (Wed Apr 29 2009 - 08:53:12 CDT)
[AMBER] (no subject) waleed zalloum (Wed Apr 29 2009 - 07:15:12 CDT)
- Re: [AMBER] (no subject) David A. Case (Wed Apr 29 2009 - 12:56:28 CDT)
[AMBER] input error in TI calculation Hannes Wallnoefer (Wed Apr 29 2009 - 10:40:58 CDT)
- Re: [AMBER] input error in TI calculation David A. Case (Wed Apr 29 2009 - 13:48:04 CDT)
[AMBER] chain restrain x TI Josmar R. da Rocha (Wed Apr 29 2009 - 17:04:52 CDT)
- Re: [AMBER] chain restrain x TI David A. Case (Thu Apr 30 2009 - 13:01:13 CDT)
  - Re: [AMBER] chain restrain x TI Josmar R. da Rocha (Sat May 02 2009 - 12:09:53 CDT)
[AMBER] Amber FF and Glycam Dong Xu (Wed Apr 29 2009 - 20:42:55 CDT)
- Re: [AMBER] Amber FF and Glycam Lachele Foley (Lists) (Thu Apr 30 2009 - 12:16:17 CDT)
- Re: [AMBER] Amber FF and Glycam Carlos Simmerling (Thu Apr 30 2009 - 13:36:21 CDT)
  - Re: [AMBER] Amber FF and Glycam Hannes Loeffler (Fri May 01 2009 - 03:33:34 CDT)
[AMBER] MM-PBSA energy decomposition Dong Xu (Wed Apr 29 2009 - 21:03:34 CDT)
- Re: [AMBER] MM-PBSA energy decomposition Hannes Kopitz (Thu Apr 30 2009 - 05:37:35 CDT)
[AMBER] hbond-error in amber9 balaji nagarajan (Wed Apr 29 2009 - 21:09:17 CDT)
- Re: [AMBER] hbond-error in amber9 Alessandro S. Nascimento (Thu Apr 30 2009 - 05:46:02 CDT)
[AMBER] Influence about HIS-HIE-HIS-HIP Rilei Yu (Wed Apr 29 2009 - 22:25:48 CDT)
- Re: [AMBER] Influence about HIS-HIE-HIS-HIP David A. Case (Thu Apr 30 2009 - 09:27:02 CDT)
- Re: [AMBER] Influence about HIS-HIE-HIS-HIP Rilei Yu (Thu Apr 30 2009 - 19:37:17 CDT)
[AMBER] how to add charge on metal ions bharat lakhani (Thu Apr 30 2009 - 01:44:46 CDT)
[AMBER] Request an error Collins Nganou (Thu Apr 30 2009 - 12:41:48 CDT)
[AMBER] (no subject) Collins Nganou (Thu Apr 30 2009 - 14:34:36 CDT)
- Re: [AMBER] (no subject) David A. Case (Thu Apr 30 2009 - 15:16:35 CDT)
[AMBER] Make parallel test faillure Collins Nganou (Thu Apr 30 2009 - 14:36:55 CDT)
- RE: [AMBER] Make parallel test faillure Ross Walker (Thu Apr 30 2009 - 14:48:06 CDT)
RE: [Subject Filtered] [AMBER] hbond-error in amber9 8% Hopkins, Robert (Thu Apr 30 2009 - 19:02:34 CDT)
- RE: [Subject Filtered] [AMBER] hbond-error in amber9 8% Thomas Cheatham III (Fri May 01 2009 - 13:07:40 CDT)
[AMBER] unable to start xleap Jayalakshmi Sridhar (Fri May 01 2009 - 13:32:27 CDT)
- Re: [AMBER] unable to start xleap Wei Zhang (Fri May 01 2009 - 13:39:03 CDT)
[AMBER] charge of Fe-heme ¶ê» (Fri May 01 2009 - 14:08:12 CDT)
- Re: [AMBER] charge of Fe-heme David A. Case (Fri May 01 2009 - 17:52:45 CDT)
- Re: [AMBER] charge of Fe-heme FyD (Sat May 02 2009 - 11:02:48 CDT)
[AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber Ye MEI (Sat May 02 2009 - 07:00:06 CDT)
[AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber Ye MEI (Sat May 02 2009 - 07:01:20 CDT)
- Re: [AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber FyD (Sat May 02 2009 - 11:06:28 CDT)
[AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Sat May 02 2009 - 15:11:48 CDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Carlos Simmerling (Sun May 03 2009 - 06:11:07 CDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Sun May 03 2009 - 20:30:05 CDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Tue May 05 2009 - 11:33:40 CDT)
  - Re: [AMBER] equilibration stops for dimer simulation with REMD Carlos Simmerling (Tue May 05 2009 - 11:39:52 CDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Tue May 05 2009 - 12:26:09 CDT)
  - Re: [AMBER] equilibration stops for dimer simulation with REMD Carlos Simmerling (Tue May 05 2009 - 12:32:42 CDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Thu May 07 2009 - 13:35:59 CDT)
[AMBER] QM/MM assigns Cd to C, Se to S C Liu (Sat May 02 2009 - 21:09:27 CDT)
- RE: [AMBER] QM/MM assigns Cd to C, Se to S Ross Walker (Sat May 02 2009 - 23:45:41 CDT)
- RE: [AMBER] QM/MM assigns Cd to C, Se to S Ross Walker (Fri May 08 2009 - 02:16:09 CDT)
[AMBER] LCPO or Molsurf? Dong Xu (Sat May 02 2009 - 22:14:55 CDT)
[AMBER] High energy during minimization aneesh cna (Sat May 02 2009 - 23:26:16 CDT)
- Re: [AMBER] High energy during minimization David A. Case (Sun May 03 2009 - 08:40:22 CDT)
- Re: [AMBER] High energy during minimization Bill Ross (Sun May 03 2009 - 13:00:32 CDT)
  - Re: [AMBER] High energy during minimization aneesh cna (Wed May 06 2009 - 00:58:00 CDT)
    - RE: [AMBER] High energy during minimization Ross Walker (Wed May 06 2009 - 01:24:30 CDT)
[AMBER] help with RESP tutorial using antechamber and gaussian Josmar R. da Rocha (Sun May 03 2009 - 12:59:23 CDT)
[AMBER] make test.parallel.MM error Collins Nganou (Sun May 03 2009 - 16:20:51 CDT)
[AMBER] prmtop Mark M Huntress (Sun May 03 2009 - 18:20:39 CDT)
- RE: [AMBER] prmtop Ross Walker (Sun May 03 2009 - 21:18:04 CDT)
[AMBER] problem with cutoff Yunjie Zhao (Sun May 03 2009 - 22:53:00 CDT)
- RE: [AMBER] problem with cutoff Ross Walker (Mon May 04 2009 - 00:02:04 CDT)
  - Re: [AMBER] problem with cutoff Yunjie Zhao (Mon May 04 2009 - 07:58:00 CDT)
    - RE: [AMBER] problem with cutoff Ross Walker (Mon May 04 2009 - 10:35:40 CDT)
[AMBER] "Parameter file not generated" Remya S R (Mon May 04 2009 - 01:17:23 CDT)
[AMBER] Parameter file not saved Remya S R (Mon May 04 2009 - 01:30:19 CDT)
[AMBER] creating new residue adds none wanted ter Jorgen Simonsen (Mon May 04 2009 - 02:49:47 CDT)
- [AMBER] Error message for tutorial 1 (run in parallel) Catein Catherine (Mon May 04 2009 - 04:05:17 CDT)
  - Re: [AMBER] Error message for tutorial 1 (run in parallel) David A. Case (Mon May 04 2009 - 07:40:36 CDT)
    - RE: [AMBER] Error message for tutorial 1 (run in parallel) Catein Catherine (Mon May 04 2009 - 08:31:05 CDT)
- Re: [AMBER] creating new residue adds none wanted ter David A. Case (Mon May 04 2009 - 08:35:41 CDT)
  - Re: [AMBER] creating new residue adds none wanted ter Jorgen Simonsen (Mon May 04 2009 - 09:09:08 CDT)
[AMBER] MM_PBSA problem in Amber 9 Sean Zhao (Mon May 04 2009 - 04:09:14 CDT)
[AMBER] Script for parallel runs Catein Catherine (Mon May 04 2009 - 04:17:42 CDT)
- [AMBER] Script for parallel runs 2 Catein Catherine (Mon May 04 2009 - 04:41:58 CDT)
  - RE: [AMBER] Script for parallel runs 2 Ross Walker (Mon May 04 2009 - 10:39:27 CDT)
- Re: [AMBER] Script for parallel runs Gustavo Seabra (Tue May 05 2009 - 11:31:38 CDT)
[AMBER] Non-zero internal energy in single trajectory MM-PBSA calculations Dmitry Osolodkin (Mon May 04 2009 - 04:24:59 CDT)
[AMBER] normal mode analysis Hannes Wallnoefer (Mon May 04 2009 - 04:39:16 CDT)
- Re: [AMBER] normal mode analysis David A. Case (Mon May 04 2009 - 08:37:02 CDT)
  - [AMBER] Why the job idle before the sentence "| Running AMBER/MPI version on 2 nodes"? Catein Catherine (Mon May 04 2009 - 10:16:08 CDT)
  - Re: [AMBER] normal mode analysis Hannes Wallnoefer (Mon May 04 2009 - 10:56:11 CDT)
[AMBER] Parameter file not saved Remya S R (Mon May 04 2009 - 07:03:08 CDT)
- Re: [AMBER] Parameter file not saved Carlos Simmerling (Mon May 04 2009 - 07:19:14 CDT)
[AMBER] MMPBSA- interaction energy for every frame Jack Colis (Mon May 04 2009 - 09:38:38 CDT)
- RE: [AMBER] MMPBSA- interaction energy for every frame Wei Huang (Mon May 04 2009 - 09:58:26 CDT)
  - Re: [AMBER] MMPBSA- interaction energy for every frame Jack Colis (Tue May 05 2009 - 03:22:35 CDT)
[AMBER] QM/MM Syed Tarique Moin (Mon May 04 2009 - 10:32:29 CDT)
- RE: [AMBER] QM/MM Ross Walker (Mon May 04 2009 - 12:47:21 CDT)
[AMBER] xleap segmentation fault Jayalakshmi Sridhar (Mon May 04 2009 - 10:50:06 CDT)
[AMBER] Error in PMEMD run Marek Malý (Mon May 04 2009 - 20:23:33 CDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Mon May 04 2009 - 20:35:54 CDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Mon May 04 2009 - 21:19:20 CDT)
Re: [AMBER] Error in PMEMD run Robert Duke (Fri May 08 2009 - 13:14:12 CDT)
- Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 13:27:20 CDT)
Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 11:38:27 CDT)
- Re: [AMBER] Error in PMEMD run Gustavo Seabra (Fri May 08 2009 - 12:28:35 CDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 12:57:36 CDT)
[AMBER] A confusion about tutorial B1 Houyang Chen (Tue May 05 2009 - 00:01:31 CDT)
- RE: [AMBER] A confusion about tutorial B1 Ross Walker (Tue May 05 2009 - 00:18:43 CDT)
  - RE: [AMBER] A confusion about tutorial B1 Houyang Chen (Tue May 05 2009 - 00:24:39 CDT)
- Re: [AMBER] A confusion about tutorial B1 Carlos Simmerling (Tue May 05 2009 - 05:11:43 CDT)
[AMBER] Problem in production run nicholus bhattacharjee (Tue May 05 2009 - 00:50:07 CDT)
- Re: [AMBER] Problem in production run Carlos Simmerling (Tue May 05 2009 - 05:07:11 CDT)
[AMBER] Suggestion for restraining chain of a protein nicholus bhattacharjee (Tue May 05 2009 - 01:29:54 CDT)
- Re: [AMBER] Suggestion for restraining chain of a protein Carlos Simmerling (Tue May 05 2009 - 05:05:16 CDT)
  - Re: [AMBER] Suggestion for restraining chain of a protein nicholus bhattacharjee (Tue May 05 2009 - 07:20:44 CDT)
    - Re: [AMBER] Suggestion for restraining chain of a protein Carlos Simmerling (Tue May 05 2009 - 07:27:05 CDT)
[AMBER] Charge problem Remya S R (Tue May 05 2009 - 06:43:47 CDT)
- Re: [AMBER] Charge problem Carlos Simmerling (Tue May 05 2009 - 07:16:32 CDT)
  - Re: [AMBER] Charge problem Remya S R (Tue May 05 2009 - 07:19:51 CDT)
    - Re: [AMBER] Charge problem Carlos Simmerling (Tue May 05 2009 - 07:58:31 CDT)
[AMBER] Problems with PMEMD installation for AMBER10 German Erlenkamp (Tue May 05 2009 - 07:40:56 CDT)
- Re: [AMBER] Problems with PMEMD installation for AMBER10 Robert Duke (Tue May 05 2009 - 08:00:54 CDT)
  - Re: [AMBER] Problems with PMEMD installation for AMBER10 German Erlenkamp (Tue May 05 2009 - 08:07:13 CDT)
    - Re: [AMBER] Problems with PMEMD installation for AMBER10 Robert Duke (Tue May 05 2009 - 08:48:06 CDT)
    - Re: [AMBER] Problems with PMEMD installation for AMBER10 German Erlenkamp (Thu May 07 2009 - 02:18:36 CDT)
[AMBER] skip parallel test Collins Nganou (Tue May 05 2009 - 08:09:00 CDT)
- Re: [AMBER] skip parallel test David A. Case (Tue May 05 2009 - 10:34:14 CDT)
- RE: [AMBER] skip parallel test Ross Walker (Tue May 05 2009 - 10:43:34 CDT)
[AMBER] Can bond clevage & formation conducted by qm/mm via sander? sychen (Tue May 05 2009 - 08:12:32 CDT)
- Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander? Gustavo Seabra (Tue May 05 2009 - 12:04:37 CDT)
- Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander? Mahmoud A. A. Ibrahim (Tue May 05 2009 - 12:15:18 CDT)
  - Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander? Gustavo Seabra (Tue May 05 2009 - 12:28:10 CDT)
[AMBER] Error: cannot run prepgen Rose Tamil (Tue May 05 2009 - 10:20:52 CDT)
[AMBER] difference in temperature Naser Alijabbari (Tue May 05 2009 - 19:02:28 CDT)
- Re: [AMBER] difference in temperature David A. Case (Wed May 06 2009 - 07:08:01 CDT)
  - Re: [AMBER] difference in temperature Naser Alijabbari (Wed May 06 2009 - 07:29:48 CDT)
[AMBER] ntf, ntc with softcore potentials and TI in amber10 Matthew Wilce (Tue May 05 2009 - 20:33:28 CDT)
- Re: [AMBER] ntf, ntc with softcore potentials and TI in amber10 steinbrt_at_rci.rutgers.edu (Tue May 05 2009 - 22:39:02 CDT)
[AMBER] Error in MM PBSA Vikas Sharma (Wed May 06 2009 - 03:35:57 CDT)
[AMBER] Conformation of sulfated Glucosamine Neha Gandhi (Wed May 06 2009 - 04:54:31 CDT)
- RE: [AMBER] Conformation of sulfated Glucosamine Matthew Tessier (Wed May 06 2009 - 10:19:22 CDT)
[AMBER] positive value of binding enrgy after MM PBSA Vikas Sharma (Wed May 06 2009 - 10:07:03 CDT)
[AMBER] xleap input pdb problem Majeed Shaik (Wed May 06 2009 - 13:47:45 CDT)
- Re: [AMBER] xleap input pdb problem David A. Case (Wed May 06 2009 - 21:16:10 CDT)
  - [AMBER] Error in parallel run Catein Catherine (Wed May 06 2009 - 21:46:02 CDT)
  - [AMBER] AMBER for dual core processor? Catein Catherine (Thu May 07 2009 - 03:05:17 CDT)
    - RE: [AMBER] AMBER for dual core processor? Ross Walker (Thu May 07 2009 - 10:26:09 CDT)
[AMBER] multiple chain specification in Sander Siddharth Rastogi (Wed May 06 2009 - 22:17:57 CDT)
- Re: [AMBER] multiple chain specification in Sander Carlos Simmerling (Thu May 07 2009 - 05:19:09 CDT)
  - Re: [AMBER] multiple chain specification in Sander Siddharth Rastogi (Thu May 07 2009 - 15:29:28 CDT)
[AMBER] ptraj PCA - Highest Eigenvalues or First 2 Calculated? Patrick Gedeon (Wed May 06 2009 - 23:12:39 CDT)
- Re: [AMBER] ptraj PCA - Highest Eigenvalues or First 2 Calculated? Hannes Loeffler (Thu May 07 2009 - 02:47:23 CDT)
[AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Thu May 07 2009 - 00:47:33 CDT)
- Re: [AMBER] Error in binding energy (MM PBSA) David A. Case (Thu May 07 2009 - 06:33:20 CDT)
  - Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Thu May 07 2009 - 08:29:22 CDT)
- RE: [AMBER] Error in binding energy (MM PBSA) Ray Luo (Thu May 07 2009 - 13:12:18 CDT)
  - Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Fri May 08 2009 - 01:42:32 CDT)
    - RE: [AMBER] Error in binding energy (MM PBSA) Ray Luo (Fri May 08 2009 - 11:42:58 CDT)
  - Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Fri May 08 2009 - 01:50:40 CDT)
[AMBER] free enrgy error in MM PBSA Vikas Sharma (Thu May 07 2009 - 05:11:44 CDT)
[AMBER] dftb_disper problem Fernando Martín García (Thu May 07 2009 - 07:30:25 CDT)
- Re: [AMBER] dftb_disper problem Gustavo Seabra (Thu May 07 2009 - 08:01:42 CDT)
  - Re: [Barracuda SPAM] Re: [AMBER] dftb_disper problem Fernando Martín García (Thu May 07 2009 - 08:32:06 CDT)
  - Re: [AMBER] dftb_disper problem Fernando Martín García (Fri May 08 2009 - 07:43:19 CDT)
[AMBER] ambertools for NAMD Jorgen Simonsen (Thu May 07 2009 - 07:35:24 CDT)
- Re: [AMBER] ambertools for NAMD Carlos Simmerling (Thu May 07 2009 - 08:36:27 CDT)
  - Re: [AMBER] ambertools for NAMD David A. Case (Thu May 07 2009 - 09:09:55 CDT)
[AMBER] Problems in the result of MM_PBSA Sean Zhao (Thu May 07 2009 - 20:30:24 CDT)
- RE: [AMBER] Problems in the result of MM_PBSA Ray Luo (Thu May 07 2009 - 21:02:58 CDT)
- Re: [AMBER] Problems in the result of MM_PBSA David A. Case (Fri May 08 2009 - 07:45:19 CDT)
  - Re: [AMBER] Problems in the result of MM_PBSA Sean Zhao (Fri May 08 2009 - 22:44:29 CDT)
[AMBER] RE: Listing gaff parameters in frcmod Bokun Cho (Thu May 07 2009 - 23:20:46 CDT)
- RE: [AMBER] RE: Listing gaff parameters in frcmod Ross Walker (Thu May 07 2009 - 23:34:08 CDT)
  - Re: [AMBER] RE: Listing gaff parameters in frcmod Bokun Cho (Fri May 08 2009 - 00:00:47 CDT)
    - Re: [AMBER] RE: Listing gaff parameters in frcmod steinbrt_at_rci.rutgers.edu (Fri May 08 2009 - 09:23:45 CDT)
[AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Fri May 08 2009 - 01:44:33 CDT)
- Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Sat May 09 2009 - 02:19:20 CDT)
  - RE: [AMBER] Error in binding energy (MM PBSA) Ray Luo (Sat May 09 2009 - 20:39:05 CDT)
    - Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Sun May 10 2009 - 04:03:07 CDT)
- Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Sat May 09 2009 - 02:20:09 CDT)
- Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Mon May 11 2009 - 03:08:28 CDT)
  - RE: [AMBER] Error in binding energy (MM PBSA) Ray Luo (Mon May 11 2009 - 13:14:20 CDT)
[AMBER] Re: Marek Malý (Fri May 08 2009 - 14:12:39 CDT)
[AMBER] Can I use only a single point calculation to derive RESP charges? Josmar R. da Rocha (Fri May 08 2009 - 19:08:54 CDT)
- Re: [AMBER] Can I use only a single point calculation to derive RESP charges? FyD (Sat May 09 2009 - 01:00:36 CDT)
  - Re: [AMBER] Can I use only a single point calculation to derive RESP charges? Josmar R. da Rocha (Sat May 09 2009 - 10:19:07 CDT)
    - Re: [AMBER] Can I use only a single point calculation to derive RESP charges? FyD (Sun May 10 2009 - 01:52:12 CDT)
[AMBER] Modifying a water molecule Jorgen Simonsen (Sat May 09 2009 - 08:16:54 CDT)
[AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. todd_at_semichem.com (Sat May 09 2009 - 11:27:52 CDT)
- Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. Adrian Roitberg (Sat May 09 2009 - 13:07:08 CDT)
  - Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. todd_at_semichem.com (Sat May 09 2009 - 13:36:17 CDT)
    - Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. FyD (Sun May 10 2009 - 00:49:55 CDT)
    - Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. todd_at_semichem.com (Sun May 10 2009 - 16:56:24 CDT)
[AMBER] molsurf and probe radius David Watson (Sat May 09 2009 - 12:32:43 CDT)
- Re: [AMBER] molsurf and probe radius David A. Case (Mon May 11 2009 - 10:03:10 CDT)
[AMBER] xleap, mac number problem Mark M Huntress (Sat May 09 2009 - 14:46:46 CDT)
- [AMBER] RE: xleap, mac number problem Mark M Huntress (Sat May 09 2009 - 17:29:50 CDT)
[AMBER] please help me out Nancy (Sun May 10 2009 - 02:56:33 CDT)
- Re: [AMBER] please help me out FyD (Mon Mar 09 2009 - 05:05:06 CDT)
  - Re: [AMBER] please help me out bharat lakhani (Thu Mar 12 2009 - 01:04:00 CDT)
- Re: [AMBER] please help me out Wei Zhang (Sun May 10 2009 - 08:21:06 CDT)
[AMBER] MM-PBSA statistics Musa Ozboyaci (Sun May 10 2009 - 05:00:19 CDT)
[AMBER] The resonable way to create single strand DNA with NAB ? Marek Malý (Sun May 10 2009 - 12:12:09 CDT)
- Re: [AMBER] The resonable way to create single strand DNA with NAB ? David A. Case (Mon May 11 2009 - 06:34:16 CDT)
  - Re: [AMBER] The resonable way to create single strand DNA with NAB ? Marek Malý (Mon May 11 2009 - 07:18:06 CDT)
[AMBER] building quadruplex with NAB Peter Varnai (Sun May 10 2009 - 18:27:38 CDT)
- Re: [AMBER] building quadruplex with NAB David A. Case (Wed May 13 2009 - 06:48:38 CDT)
  - Re: [AMBER] building quadruplex with NAB Peter Varnai (Tue Oct 27 2009 - 15:00:09 CDT)
    - Re: [AMBER] building quadruplex with NAB case (Tue Oct 27 2009 - 21:23:29 CDT)
[AMBER] Adding non standard residues Jorgen Simonsen (Mon May 11 2009 - 03:54:25 CDT)
- Re: [AMBER] Adding non standard residues David A. Case (Mon May 11 2009 - 12:30:56 CDT)
  - Re: [AMBER] Adding non standard residues Jorgen Simonsen (Mon May 11 2009 - 16:11:49 CDT)
[AMBER] molecular crystal simulation Simona Irrera (Tue May 12 2009 - 06:04:26 CDT)
- Re: [AMBER] molecular crystal simulation David A. Case (Wed May 13 2009 - 17:28:37 CDT)
[AMBER] ptraj netcdf Bala subramanian (Tue May 12 2009 - 07:04:00 CDT)
- Re: [AMBER] ptraj netcdf Chris Moth (Tue May 12 2009 - 10:46:31 CDT)
  - [AMBER] anal output: Entalphy or Free Energy? E.M. (Tue May 12 2009 - 17:25:41 CDT)
[AMBER] anal output: Entalphy or Free Energy? Edward M (Tue May 12 2009 - 19:14:37 CDT)
[AMBER] Question about Thermal Integration with Softcore Elodie Laine (Wed May 13 2009 - 04:13:22 CDT)
- Re: [AMBER] Question about Thermal Integration with Softcore steinbrt_at_rci.rutgers.edu (Wed May 13 2009 - 10:11:16 CDT)
[AMBER] amber9 in fedora10 Bala subramanian (Wed May 13 2009 - 04:50:25 CDT)
- RE: [AMBER] amber9 in fedora10 Ross Walker (Wed May 13 2009 - 18:22:20 CDT)
[AMBER] essential dynamics Chunliyan (Wed May 13 2009 - 11:23:23 CDT)
- Re: [AMBER] essential dynamics David A. Case (Wed May 13 2009 - 12:15:50 CDT)
[AMBER] re: essential dynamics Chunliyan (Wed May 13 2009 - 12:25:57 CDT)
- Re: [AMBER] re: essential dynamics David A. Case (Wed May 13 2009 - 12:48:42 CDT)
  - RE: [AMBER] re: essential dynamics Niel Henriksen (Wed May 13 2009 - 13:28:22 CDT)
[AMBER] normal modes calculation Neha Gandhi (Wed May 13 2009 - 22:12:13 CDT)
- Re: [AMBER] normal modes calculation chaitanya koppisetty (Thu May 14 2009 - 03:51:28 CDT)
[AMBER] Amber - Leap- SolvateBox help Shubhra Gupta (Thu May 14 2009 - 00:04:16 CDT)
- RE: [AMBER] Amber - Leap- SolvateBox help Ross Walker (Thu May 14 2009 - 07:28:36 CDT)
- Re: [AMBER] Amber - Leap- SolvateBox help David A. Case (Fri May 15 2009 - 18:57:00 CDT)
- Re: [AMBER] Amber - Leap- SolvateBox help Shubhra Gupta (Mon May 18 2009 - 22:54:23 CDT)
  - Re: [AMBER] Amber - Leap- SolvateBox help David A. Case (Tue May 19 2009 - 06:48:39 CDT)
- Re: [AMBER] Amber - Leap- SolvateBox help Remya S R (Tue May 19 2009 - 01:22:12 CDT)
- RE: [AMBER] Amber - Leap- SolvateBox help Ross Walker (Wed May 20 2009 - 00:20:50 CDT)
[AMBER] pmemd running very slow in amber10 Vijay Manickam Achari (Thu May 14 2009 - 00:41:40 CDT)
- Re: [AMBER] pmemd running very slow in amber10 Carlos Simmerling (Thu May 14 2009 - 05:09:11 CDT)
  - RE: [AMBER] pmemd running very slow in amber10 Ross Walker (Thu May 14 2009 - 07:57:43 CDT)
- Re: [AMBER] pmemd running very slow in amber10 Robert Duke (Thu May 14 2009 - 08:38:29 CDT)
Re: [OFFLIST] Re: [AMBER] amber9 in fedora10 Bala subramanian (Thu May 14 2009 - 03:18:07 CDT)
[AMBER] MM-PBSA tutorial Workalemhu Berhanu (Thu May 14 2009 - 12:16:55 CDT)
- Re: [AMBER] MM-PBSA tutorial steinbrt_at_rci.rutgers.edu (Thu May 14 2009 - 12:26:50 CDT)
  - Re: [AMBER] MM-PBSA tutorial Cihan Aydin (Thu May 14 2009 - 20:19:04 CDT)
- Re: [AMBER] MM-PBSA tutorial Workalemhu Berhanu (Thu May 14 2009 - 13:53:25 CDT)
[AMBER] xmin Peter Varnai (Thu May 14 2009 - 16:29:09 CDT)
- Re: [AMBER] xmin Scott Brozell (Sun May 17 2009 - 15:45:27 CDT)
  - [AMBER] What is the purpose to do the bond constraints? Chih-Ying Lin (Sun May 17 2009 - 17:09:04 CDT)
  - Re: [AMBER] xmin Peter Varnai (Sun May 17 2009 - 19:58:00 CDT)
    - Re: [AMBER] xmin Scott Brozell (Mon May 18 2009 - 15:30:17 CDT)
[AMBER] Fw: MM-PBSA with explicit water mathew k varghese (Fri May 15 2009 - 01:43:46 CDT)
[AMBER] MM-PBSA with explicit water mathew k varghese (Fri May 15 2009 - 01:45:23 CDT)
[AMBER] xleap reading hydrogens giving error Jorgen Simonsen (Fri May 15 2009 - 02:47:10 CDT)
- Re: [AMBER] xleap reading hydrogens giving error David A. Case (Fri May 15 2009 - 09:17:04 CDT)
  - Re: [AMBER] xleap reading hydrogens giving error Jorgen Simonsen (Fri May 15 2009 - 10:54:17 CDT)
    - Re: [AMBER] xleap reading hydrogens giving error David A. Case (Fri May 15 2009 - 11:25:11 CDT)
    - [AMBER] how to make the different/specific displacement of ligand around protein? Chih-Ying Lin (Fri May 15 2009 - 18:55:49 CDT)
[AMBER] scee term Neha Gandhi (Fri May 15 2009 - 04:03:48 CDT)
- RE: [AMBER] scee term Ross Walker (Fri May 15 2009 - 10:02:09 CDT)
[AMBER] adding a standard amino acid as ligand sheerychen (Fri May 15 2009 - 04:37:51 CDT)
- Re: [AMBER] adding a standard amino acid as ligand FyD (Fri May 15 2009 - 08:39:18 CDT)
[AMBER] secstruct with ptraj Bala subramanian (Fri May 15 2009 - 05:19:54 CDT)
[AMBER] Issue related to vector saving S.Sundar Raman (Fri May 15 2009 - 08:35:01 CDT)
[AMBER] MM-GBSA energy decomposition and pairwise decomposition question Dong Xu (Fri May 15 2009 - 17:05:52 CDT)
[AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4' ben rodriguez (Fri May 15 2009 - 17:09:44 CDT)
- Re: [AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4' David A. Case (Fri May 15 2009 - 18:56:34 CDT)
[AMBER] Alignment of small molecule on peptide fragment Workalemhu Berhanu (Sat May 16 2009 - 04:31:08 CDT)
[AMBER] Alignment of small molecule on peptide fragment Workalemhu Berhanu (Sat May 16 2009 - 04:32:38 CDT)
[AMBER] Issue related to saving the vector in ptraj S.Sundar Raman (Sat May 16 2009 - 07:41:10 CDT)
- [AMBER] How to setup the pH value? Chih-Ying Lin (Sat May 16 2009 - 12:29:21 CDT)
  - Re: [AMBER] How to setup the pH value? David A. Case (Tue May 19 2009 - 14:08:53 CDT)
    - [AMBER] What are the elements to speed up the simulation? Chih-Ying Lin (Tue May 19 2009 - 17:17:07 CDT)
[AMBER] Amber 10 install parallel problem Hopkins, Robert (Sat May 16 2009 - 19:38:16 CDT)
[AMBER] Running PTRAJ command line scripts in background Hopkins, Robert (Sat May 16 2009 - 19:47:38 CDT)
- Re: [AMBER] Running PTRAJ command line scripts in background Jia Xu (Sun May 17 2009 - 02:16:49 CDT)
  - RE: [AMBER] Running PTRAJ command line scripts in background Hopkins, Robert (Sun May 17 2009 - 11:55:48 CDT)
- RE: [AMBER] Running PTRAJ command line scripts in background Ross Walker (Sun May 17 2009 - 22:35:09 CDT)
  - RE: [AMBER] Running PTRAJ command line scripts in background Hopkins, Robert (Mon May 18 2009 - 17:50:06 CDT)
[AMBER] makeDIST_RST: no map function for ambiguous restraint Peter Varnai (Sun May 17 2009 - 13:41:24 CDT)
- Re: [AMBER] makeDIST_RST: no map function for ambiguous restraint David A. Case (Tue May 19 2009 - 07:35:31 CDT)
  - Re: [AMBER] makeDIST_RST: no map function for ambiguous restraint Peter Varnai (Mon Jun 01 2009 - 14:49:36 CDT)
[AMBER] parallel amber on cluster Siavoush Dastmalchi (Mon May 18 2009 - 01:04:58 CDT)
- Re: [AMBER] parallel amber on cluster David A. Case (Mon May 18 2009 - 06:54:18 CDT)
[AMBER] Problem in Nmode Kshatresh Dutta Dubey (Mon May 18 2009 - 01:07:52 CDT)
[AMBER] Modification of His Jorgen Simonsen (Mon May 18 2009 - 05:51:50 CDT)
- Re: [AMBER] Modification of His David A. Case (Mon May 18 2009 - 06:58:34 CDT)
  - Re: [AMBER] Modification of His Jorgen Simonsen (Mon May 18 2009 - 07:16:10 CDT)
    - Re: [AMBER] Modification of His David A. Case (Mon May 18 2009 - 07:31:33 CDT)
- Re: [AMBER] Modification of His Bill Ross (Mon May 18 2009 - 15:06:16 CDT)
[AMBER] Error running MM _PBSA.pl script Vikas Sharma (Mon May 18 2009 - 07:00:13 CDT)
- å›žå¤ï¼š [AMBER] Error running MM _PBSA.pl script å»–é’åŽ (Mon May 18 2009 - 07:08:47 CDT)
  - Re: å›žå¤ï¼š [AMBER] Error running MM _PBSA.pl script Vikas Sharma (Mon May 18 2009 - 09:06:49 CDT)
    - å›žå¤ï¼š å›žå¤ï¼š [AMBER] Error running MM _PBSA.pl script å»–é’åŽ (Mon May 18 2009 - 09:41:14 CDT)
- RE: [AMBER] Error running MM _PBSA.pl script Ray Luo (Mon May 18 2009 - 12:43:30 CDT)
  - Re: [AMBER] Error running MM _PBSA.pl script Vikas Sharma (Mon May 18 2009 - 23:34:18 CDT)
    - Re: [AMBER] Error running MM _PBSA.pl script liuhui (Tue May 19 2009 - 09:29:23 CDT)
- Re: [AMBER] Error running MM _PBSA.pl script Vikas Sharma (Tue May 19 2009 - 10:02:21 CDT)
  - Re: [AMBER] Error running MM _PBSA.pl script liuhui (Tue May 19 2009 - 11:15:24 CDT)
[AMBER] problem with parmchk rebeca (Mon May 18 2009 - 08:59:51 CDT)
- Re: [AMBER] problem with parmchk David A. Case (Mon May 18 2009 - 09:19:54 CDT)
  - Re: [AMBER] problem with parmchk rebeca (Mon May 18 2009 - 09:34:31 CDT)
    - Re: [AMBER] problem with parmchk David A. Case (Mon May 18 2009 - 15:00:07 CDT)
[AMBER] no equilibrium Nancy (Mon May 18 2009 - 21:32:01 CDT)
[AMBER] no equilibrium Nancy (Mon May 18 2009 - 21:44:03 CDT)
- Re: [AMBER] no equilibrium steinbrt_at_rci.rutgers.edu (Mon May 18 2009 - 22:00:40 CDT)
[AMBER] The largest AMBER calculation(s)? Vlad (Mon May 18 2009 - 21:58:27 CDT)
[AMBER] Problem with Nmode Kshatresh Dutta Dubey (Mon May 18 2009 - 23:25:05 CDT)
- Re: [AMBER] Problem with Nmode David A. Case (Wed May 20 2009 - 13:02:44 CDT)
  - Re: [AMBER] Problem with Nmode Kshatresh Dutta Dubey (Thu May 21 2009 - 00:14:50 CDT)
    - Re: [AMBER] Problem with Nmode David A. Case (Thu May 21 2009 - 07:29:06 CDT)
[AMBER] AMBER 10 output Sergey Samsonov (Tue May 19 2009 - 02:33:21 CDT)
- Re: [AMBER] AMBER 10 output steinbrt_at_rci.rutgers.edu (Tue May 19 2009 - 08:53:03 CDT)
  - Re: [AMBER] AMBER 10 output Sergey Samsonov (Tue May 19 2009 - 09:53:41 CDT)
[AMBER] Problem with nonstandard residues moitrayee_at_mbu.iisc.ernet.in (Tue May 19 2009 - 06:48:33 CDT)
- Re: [AMBER] Problem with nonstandard residues David A. Case (Tue May 19 2009 - 07:54:14 CDT)
  - Re: [AMBER] Problem with nonstandard residues moitrayee_at_mbu.iisc.ernet.in (Tue May 19 2009 - 08:10:00 CDT)
    - Re: [AMBER] Problem with nonstandard residues David A. Case (Tue May 19 2009 - 10:22:15 CDT)
    - Re: [AMBER] Problem with nonstandard residues moitrayee_at_mbu.iisc.ernet.in (Tue May 19 2009 - 11:47:38 CDT)
[AMBER] gaff and aromatic compounds rebeca (Tue May 19 2009 - 10:50:02 CDT)
- Re: [AMBER] gaff and aromatic compounds David A. Case (Tue May 19 2009 - 11:07:29 CDT)
- Re: [AMBER] gaff and aromatic compounds Junmei Wang (Thu May 21 2009 - 20:24:52 CDT)
  - Re: [AMBER] gaff and aromatic compounds rebeca (Fri May 22 2009 - 04:04:45 CDT)
    - Re: [AMBER] gaff and aromatic compounds Junmei Wang (Tue May 26 2009 - 11:03:53 CDT)
[AMBER] loadpdb atom type Mark M Huntress (Tue May 19 2009 - 11:20:20 CDT)
- Re: [AMBER] loadpdb atom type Carlos Simmerling (Tue May 19 2009 - 12:09:29 CDT)
  - RE: [AMBER] loadpdb atom type Mark M Huntress (Tue May 19 2009 - 13:15:02 CDT)
- Re: [AMBER] loadpdb atom type David A. Case (Tue May 19 2009 - 13:19:44 CDT)
[AMBER] Tutorial A1 Workalemhu Berhanu (Tue May 19 2009 - 18:05:15 CDT)
[AMBER] resp charge R. A. (Tue May 19 2009 - 21:35:25 CDT)
- [AMBER] resp charge FyD (Wed May 20 2009 - 02:42:07 CDT)
- RE: [AMBER] resp charge Ross Walker (Wed May 20 2009 - 10:05:20 CDT)
[AMBER] gaff and aromatic compounds rebeca (Wed May 20 2009 - 03:54:43 CDT)
- Re: [AMBER] gaff and aromatic compounds David A. Case (Wed May 20 2009 - 07:04:05 CDT)
[AMBER] MM PBSA output Vikas Sharma (Wed May 20 2009 - 06:53:57 CDT)
- å›žå¤ï¼š [AMBER] MM PBSA output å»–é’åŽ (Wed May 20 2009 - 07:15:04 CDT)
  - Re: å›žå¤ï¼š [AMBER] MM PBSA output Vikas Sharma (Wed May 20 2009 - 12:54:32 CDT)
[AMBER] Amber/CHARMM summer school David A. Case (Wed May 20 2009 - 07:40:39 CDT)
- RE: [AMBER] Amber/CHARMM summer school CHAMI F. (Thu May 21 2009 - 06:56:23 CDT)
[AMBER] ptraj questions Jia Xu (Wed May 20 2009 - 09:39:13 CDT)
- Re: [AMBER] ptraj questions Myunggi Yi (Fri May 22 2009 - 08:57:08 CDT)
  - Re: [AMBER] ptraj questions Jia Xu (Sun May 24 2009 - 00:06:10 CDT)
[AMBER] RE: add magnesium Ross Walker (Wed May 20 2009 - 16:30:09 CDT)
[AMBER] how to use two dimensions periodic boundary ? Nancy (Wed May 20 2009 - 20:32:50 CDT)
[AMBER] errors when add ions zgong.hust (Wed May 20 2009 - 21:51:48 CDT)
- Re: [AMBER] errors when add ions David A. Case (Thu May 21 2009 - 07:23:08 CDT)
- [AMBER] Why does protein carry charges? Chih-Ying Lin (Fri May 22 2009 - 23:09:21 CDT)
  - [AMBER] How to choose the counter ions for proteins? Chih-Ying Lin (Sat May 23 2009 - 00:42:40 CDT)
    - RE: [AMBER] How to choose the counter ions for proteins? Ross Walker (Sat May 23 2009 - 13:09:27 CDT)
    - Re: RE: [AMBER] How to choose the counter ions for proteins? Chih-Ying Lin (Sat May 23 2009 - 13:16:49 CDT)
  - RE: [AMBER] Why does protein carry charges? Ross Walker (Sat May 23 2009 - 13:06:57 CDT)
[AMBER] Protein with HETATM, am I doing the nicholus bhattacharjee (Wed May 20 2009 - 23:48:42 CDT)
- Re: [AMBER] Protein with HETATM, am I doing the Amit Bajaj (Thu May 21 2009 - 00:26:49 CDT)
  - Re: [AMBER] Protein with HETATM, am I doing the nicholus bhattacharjee (Thu May 21 2009 - 01:43:37 CDT)
    - Re: [AMBER] Protein with HETATM, am I doing the amit (Mon May 25 2009 - 10:26:15 CDT)
[AMBER] Radius for Bromine in MMPBSA calculation john smith (Thu May 21 2009 - 00:24:05 CDT)
- RE: [AMBER] Radius for Bromine in MMPBSA calculation Ray Luo (Thu May 21 2009 - 11:32:41 CDT)
  - Re: [AMBER] Radius for Bromine in MMPBSA calculation john smith (Sun May 24 2009 - 23:52:48 CDT)
[AMBER] Protein with HETATM, am I doing the right thing nicholus bhattacharjee (Thu May 21 2009 - 06:21:15 CDT)
- Re: [AMBER] Protein with HETATM, am I doing the right thing David A. Case (Thu May 21 2009 - 07:39:14 CDT)
  - Re: [AMBER] Protein with HETATM, am I doing the right thing nicholus bhattacharjee (Thu May 21 2009 - 11:28:52 CDT)
[AMBER] Loading PDB of complex Vikas Sharma (Thu May 21 2009 - 08:13:36 CDT)
- Re: [AMBER] Loading PDB of complex Carlos Simmerling (Thu May 21 2009 - 08:48:06 CDT)
  - Re: [AMBER] Loading PDB of complex Vikas Sharma (Fri May 22 2009 - 00:56:36 CDT)
[AMBER] Installation directory Thomas Spraggins (Thu May 21 2009 - 13:02:59 CDT)
- Re: [AMBER] Installation directory David A. Case (Thu May 21 2009 - 13:19:28 CDT)
  - Re: [AMBER] Installation directory Thomas Spraggins (Thu May 21 2009 - 14:18:13 CDT)
    - Re: [AMBER] Installation directory Atro Tossavainen (Mon May 25 2009 - 03:10:34 CDT)
[AMBER] Segmentation error in Ptraj Kshatresh Dutta Dubey (Fri May 22 2009 - 02:17:27 CDT)
[AMBER] lipid membrane(dppc) in amber xueqin pang (Fri May 22 2009 - 03:42:54 CDT)
- Re: [AMBER] lipid membrane(dppc) in amber Myunggi Yi (Fri May 22 2009 - 08:45:20 CDT)
[AMBER] lipid membrane(dppc) in amber xueqin pang (Fri May 22 2009 - 04:01:26 CDT)
[AMBER] decomposition and alanine scanning å»–é’åŽ (Fri May 22 2009 - 09:13:49 CDT)
[AMBER] MMPBSA extract coordinate vijayaraj_at_clri.res.in (Fri May 22 2009 - 13:00:57 CDT)
[AMBER] Nab units ? Marek Maly (Fri May 22 2009 - 19:20:14 CDT)
- Re: [AMBER] Nab units ? David A. Case (Fri May 22 2009 - 20:33:34 CDT)
  - Re: [AMBER] Nab units ? Marek Maly (Fri May 22 2009 - 20:43:41 CDT)
[AMBER] 2 atoms not in residue template Workalemhu Berhanu (Sat May 23 2009 - 19:11:12 CDT)
[AMBER] file contains 2 atoms not in residue templates Workalemhu Berhanu (Sat May 23 2009 - 19:17:09 CDT)
- Re: [AMBER] file contains 2 atoms not in residue templates David A. Case (Sun May 24 2009 - 08:12:14 CDT)
[AMBER] problem with MM-PBSA Maryam Hamzehee (Sat May 23 2009 - 23:48:05 CDT)
[AMBER] nanoseconds of simulation with nscm=0 Naser Alijabbari (Sun May 24 2009 - 12:20:18 CDT)
- Re: [AMBER] nanoseconds of simulation with nscm=0 Thomas Cheatham (Sun May 24 2009 - 13:27:33 CDT)
  - Re: [AMBER] nanoseconds of simulation with nscm=0 Naser Alijabbari (Sun May 24 2009 - 14:56:28 CDT)
    - Re: [AMBER] nanoseconds of simulation with nscm=0 Thomas Cheatham (Sun May 24 2009 - 15:37:23 CDT)
[AMBER] Unit 8 Error on OPEN: prmtop Workalemhu Berhanu (Sun May 24 2009 - 12:27:38 CDT)
- Re: [AMBER] Unit 8 Error on OPEN: prmtop Peter Gannett (Sun May 24 2009 - 12:46:47 CDT)
- Re: [AMBER] Unit 8 Error on OPEN: prmtop Alessandro Nascimento (Sun May 24 2009 - 13:28:26 CDT)
  - Re: [AMBER] Unit 8 Error on OPEN: prmtop Peter Gannett (Sun May 24 2009 - 14:29:58 CDT)
  - Re: [AMBER] Unit 8 Error on OPEN: prmtop Workalemhu Berhanu (Sun May 24 2009 - 17:12:00 CDT)
[AMBER] Strange high temperature in softcore TI Tom Joseph (Sun May 24 2009 - 20:54:43 CDT)
- Re: [AMBER] Strange high temperature in softcore TI steinbrt_at_rci.rutgers.edu (Sun May 24 2009 - 21:26:28 CDT)
  - Re: [AMBER] Strange high temperature in softcore TI Tom Joseph (Sun May 24 2009 - 22:20:20 CDT)
    - Re: [AMBER] Strange high temperature in softcore TI steinbrt_at_rci.rutgers.edu (Sun May 24 2009 - 23:13:38 CDT)
[AMBER] How to know that the md is stable in equilibration run nicholus bhattacharjee (Mon May 25 2009 - 06:54:25 CDT)
- [AMBER] Re: How to know that the md is stable in equilibration run nicholus bhattacharjee (Mon May 25 2009 - 11:11:39 CDT)
[AMBER] Problem with MM-PBSA energy calculation Rubben Torella (Mon May 25 2009 - 10:58:41 CDT)
- Re: [AMBER] Problem with MM-PBSA energy calculation Barbault Florent (Mon May 25 2009 - 13:57:19 CDT)
  - Re: [AMBER] Problem with MM-PBSA energy calculation Rubben Torella (Tue May 26 2009 - 06:24:56 CDT)
[AMBER] hbond_ptraj balaji nagarajan (Mon May 25 2009 - 15:05:12 CDT)
- Re: [AMBER] hbond_ptraj Thomas Cheatham (Wed May 27 2009 - 19:39:15 CDT)
[AMBER] Question about &dipoles printing in AMBER 8 Karen Callahan (Mon May 25 2009 - 18:46:00 CDT)
[AMBER] partial charge and topology of intrastrand cross-link DNA Shuang Ding (Mon May 25 2009 - 21:27:43 CDT)
- Re: [AMBER] partial charge and topology of intrastrand cross-link DNA FyD (Wed May 27 2009 - 00:27:40 CDT)
[AMBER] problem with MM-PBSA Maryam Hamzehee (Mon May 25 2009 - 23:52:29 CDT)
- Re: [AMBER] problem with MM-PBSA David A. Case (Tue May 26 2009 - 06:37:31 CDT)
- RE: [AMBER] problem with MM-PBSA Ray Luo (Tue May 26 2009 - 11:44:14 CDT)
- Re: [AMBER] problem with MM-PBSA Thomas Cheatham (Wed May 27 2009 - 19:35:30 CDT)
- Re: [AMBER] problem with MM-PBSA Bill Ross (Wed May 27 2009 - 19:52:19 CDT)
[AMBER] Molecular simulation of a protein using special H2O cluster Rilei Yu (Tue May 26 2009 - 03:20:56 CDT)
- Re: [AMBER] Molecular simulation of a protein using special H2O cluster Carlos Simmerling (Tue May 26 2009 - 06:45:50 CDT)
- Re: [AMBER] Molecular simulation of a protein using special H2O cluster Rilei Yu (Tue May 26 2009 - 19:21:15 CDT)
  - Re: [AMBER] Molecular simulation of a protein using special H2O cluster Carlos Simmerling (Tue May 26 2009 - 19:25:03 CDT)
[AMBER] Re: About Amber installations Alan (Tue May 26 2009 - 04:53:37 CDT)
- Re: [AMBER] Re: About Amber installations jacky zhao (Tue May 26 2009 - 06:18:25 CDT)
[AMBER] ligand QM/semi-empirical coords optmisation Alan (Tue May 26 2009 - 05:55:09 CDT)
- Re: [AMBER] ligand QM/semi-empirical coords optmisation David A. Case (Tue May 26 2009 - 06:41:25 CDT)
  - Re: [AMBER] ligand QM/semi-empirical coords optmisation Alan (Thu Jun 04 2009 - 09:19:28 CDT)
    - Re: [AMBER] ligand QM/semi-empirical coords optmisation David A. Case (Thu Jun 04 2009 - 10:06:28 CDT)
    - Re: [AMBER] ligand QM/semi-empirical coords optmisation Alan (Thu Jun 04 2009 - 13:05:27 CDT)
  - Re: [AMBER] ligand QM/semi-empirical coords optmisation Junmei Wang (Fri Jun 05 2009 - 10:01:32 CDT)
    - Re: [AMBER] ligand QM/semi-empirical coords optmisation Francesco Pietra (Fri Jun 05 2009 - 13:17:45 CDT)
[AMBER] problem with program anal within Amber10 Marina Grabar (Tue May 26 2009 - 06:48:38 CDT)
- Re: [AMBER] problem with program anal within Amber10 David A. Case (Tue May 26 2009 - 07:03:01 CDT)
[AMBER] partial charges of lipid membrane for GPCR system xueqin pang (Tue May 26 2009 - 08:34:34 CDT)
[AMBER] mdfil: Error unknown flag during sander minimization Workalemhu Berhanu (Tue May 26 2009 - 08:57:29 CDT)
- Re: [AMBER] mdfil: Error unknown flag during sander minimization David A. Case (Tue May 26 2009 - 09:05:37 CDT)
- Re: [AMBER] mdfil: Error unknown flag during sander minimization Shubhra Gupta (Tue May 26 2009 - 23:07:25 CDT)
[AMBER] RE: About Amber10 installation "Possible Failure" Ross Walker (Tue May 26 2009 - 10:38:19 CDT)
[AMBER] get typeid of -1, sleap - AMBER with amoeba ff Tomasio, Susana (Tue May 26 2009 - 10:51:18 CDT)
[AMBER] Tutorial 4 Please check the total charge and your -nc flag Workalemhu Berhanu (Tue May 26 2009 - 14:47:07 CDT)
- Re: [AMBER] Tutorial 4 Please check the total charge and your -nc flag David A. Case (Wed May 27 2009 - 06:42:29 CDT)
[AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber Workalemhu Berhanu (Tue May 26 2009 - 16:45:55 CDT)
- Re: [AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber Rubben Torella (Tue May 26 2009 - 17:33:18 CDT)
[AMBER] Re: Help with xleap Taufik Al-Sarraj (Tue May 26 2009 - 18:58:00 CDT)
[AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels Tomasio, Susana (Wed May 27 2009 - 06:25:35 CDT)
- Re: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels David A. Case (Wed May 27 2009 - 06:57:07 CDT)
  - RE: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off- different labels Tomasio, Susana (Wed May 27 2009 - 07:13:58 CDT)
[AMBER] PARMCAL calculation ? Marek Maly (Wed May 27 2009 - 09:19:48 CDT)
[AMBER] MM-PBSA and NetCDF Bradshaw, Richard (Wed May 27 2009 - 10:38:13 CDT)
[AMBER] Tutorial 4 Parameter file was not saved Workalemhu Berhanu (Wed May 27 2009 - 11:00:30 CDT)
- RE: [AMBER] Tutorial 4 Parameter file was not saved Ross Walker (Wed May 27 2009 - 12:31:30 CDT)
[AMBER] heating advice Mark M Huntress (Wed May 27 2009 - 15:44:26 CDT)
[AMBER] SANDER BOMB PRADEEP VENKATARAMAN (Wed May 27 2009 - 21:39:56 CDT)
- Re: [AMBER] SANDER BOMB David A. Case (Thu May 28 2009 - 09:29:50 CDT)
[AMBER] Changing bond length manoj singh (Wed May 27 2009 - 22:47:52 CDT)
- RE: [AMBER] Changing bond length Ross Walker (Wed May 27 2009 - 23:38:59 CDT)
  - Re: [AMBER] Changing bond length manoj singh (Thu May 28 2009 - 12:00:14 CDT)
[AMBER] AMOEBA and carbon nanotubes + include parameters Tomasio, Susana (Thu May 28 2009 - 05:23:00 CDT)
[AMBER] MM-PBSA nmode statistics Dmitry Osolodkin (Thu May 28 2009 - 06:54:18 CDT)
- Re: [AMBER] MM-PBSA nmode statistics Kshatresh Dutta Dubey (Fri May 29 2009 - 00:13:34 CDT)
  - Re: [AMBER] MM-PBSA nmode statistics Dmitry Osolodkin (Fri May 29 2009 - 05:53:27 CDT)
[AMBER] contacts in ptraj Å·ÑôµÂ·½ (Thu May 28 2009 - 06:55:28 CDT)
[AMBER] how to know that adequate equilibration from rmsd curve of equilibration nicholus bhattacharjee (Thu May 28 2009 - 08:37:29 CDT)
[AMBER] FW: About Amber10 installation "Possible Failure" Ross Walker (Thu May 28 2009 - 09:06:31 CDT)
[AMBER] Minimization error on protonated system? Please help. Thanks! Haizhen Zhong (Thu May 28 2009 - 09:58:49 CDT)
- Re: [AMBER] Minimization error on protonated system? Please help. Thanks! David A. Case (Thu May 28 2009 - 10:17:59 CDT)
[AMBER] Minimization on MM-PBSA Rubben Torella (Thu May 28 2009 - 10:23:07 CDT)
Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Bill Ross (Thu May 28 2009 - 10:42:13 CDT)
- Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration nicholus bhattacharjee (Thu May 28 2009 - 13:08:52 CDT)
  - Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Carlos Simmerling (Thu May 28 2009 - 13:15:09 CDT)
[AMBER] unnatural amino acid emiliawu_at_dicp.ac.cn (Fri May 29 2009 - 01:56:43 CDT)
- Re: [AMBER] unnatural amino acid FyD (Thu May 28 2009 - 13:46:27 CDT)
[AMBER] xleap segmentation fault Jayalakshmi Sridhar (Thu May 28 2009 - 11:29:47 CDT)
- Re: [AMBER] xleap segmentation fault David A. Case (Thu May 28 2009 - 15:05:12 CDT)
- Re: [AMBER] xleap segmentation fault Jayalakshmi Sridhar (Fri May 29 2009 - 10:45:25 CDT)
[AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 13:16:35 CDT)
- RE: [AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 14:31:14 CDT)
  - Re: [AMBER] ask for parm99MOD Adrian Roitberg (Thu May 28 2009 - 14:38:23 CDT)
RE: [AMBER] question of ibelly used in pmemd Kristina Furse (Mon Jul 20 2009 - 11:56:26 CDT)
- Re: [AMBER] question of ibelly used in pmemd Robert Duke (Mon Jul 20 2009 - 12:10:03 CDT)
- RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Mon Jul 20 2009 - 12:20:36 CDT)
  - RE: [AMBER] question of ibelly used in pmemd Ross Walker (Mon Jul 20 2009 - 12:32:08 CDT)
    - RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Mon Jul 20 2009 - 12:39:16 CDT)
    - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Mon Jul 20 2009 - 12:55:23 CDT)
  - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Tue Jul 21 2009 - 08:15:20 CDT)
RE: [AMBER] question of ibelly used in pmemd Ross Walker (Wed Jul 15 2009 - 20:32:07 CDT)
- RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Fri Jul 17 2009 - 09:36:06 CDT)
[AMBER] How to take into account the charge in GAFF parameterization Workalemhu Berhanu (Thu May 28 2009 - 18:22:07 CDT)
- Re: [AMBER] How to take into account the charge in GAFF parameterization cgji (Fri May 29 2009 - 01:49:44 CDT)
[AMBER] J coupling constant calculation Neha Gandhi (Fri May 29 2009 - 00:24:37 CDT)
- Re: [AMBER] J coupling constant calculation Dechang Li (Fri May 29 2009 - 00:31:06 CDT)
- Re: [AMBER] J coupling constant calculation Gustavo Seabra (Tue Jun 02 2009 - 09:18:08 CDT)
[AMBER] broken Ligand Shubhra Gupta (Fri May 29 2009 - 08:28:22 CDT)
- Re: [AMBER] broken Ligand David A. Case (Fri May 29 2009 - 09:45:20 CDT)
  - Re: [AMBER] broken Ligand Shubhra Gupta (Sat May 30 2009 - 01:35:46 CDT)
    - Re: [AMBER] broken Ligand David A. Case (Sun May 31 2009 - 07:50:57 CDT)
[AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Fri May 29 2009 - 09:02:31 CDT)
- Re: [AMBER] QQD psuedoatom restraints David A. Case (Fri May 29 2009 - 10:18:29 CDT)
  - RE: [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Fri May 29 2009 - 14:01:34 CDT)
    - Re: [AMBER] QQD psuedoatom restraints David A. Case (Fri May 29 2009 - 14:26:27 CDT)
    - RE: [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Mon Jun 01 2009 - 06:21:19 CDT)
  - RE: [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Fri Jun 12 2009 - 13:51:25 CDT)
    - Re: [AMBER] QQD psuedoatom restraints David A. Case (Mon Jun 15 2009 - 07:00:23 CDT)
[AMBER] Targeted MD and QM/MM Gabriel Urquiza (Fri May 29 2009 - 15:09:31 CDT)
- [AMBER] protein molecular weight? Chih-Ying Lin (Fri May 29 2009 - 17:44:24 CDT)
  - Re: [AMBER] protein molecular weight? Tom Joseph (Fri May 29 2009 - 18:40:58 CDT)
- Re: [AMBER] Targeted MD and QM/MM Gustavo Seabra (Tue Jun 02 2009 - 09:43:35 CDT)
  - Re: [AMBER] Targeted MD and QM/MM Gabriel Urquiza (Tue Jun 02 2009 - 17:08:11 CDT)
[AMBER] the atom number exceeds the MAXATOM, reallocate memory automatically Workalemhu Berhanu (Sat May 30 2009 - 06:20:03 CDT)
- Re: [AMBER] the atom number exceeds the MAXATOM, reallocate memory automatically David A. Case (Sat May 30 2009 - 08:11:59 CDT)
[AMBER] ERROR in ptrajInitializeState(): Attempting .... Siavoush Dastmalchi (Sat May 30 2009 - 11:06:51 CDT)
[AMBER] RE: ERROR in ptrajInitializeState(): Attempting .... Siavoush Dastmalchi (Sat May 30 2009 - 12:11:55 CDT)
[AMBER] Parameter file content manoj singh (Sat May 30 2009 - 20:53:37 CDT)
- Re: [AMBER] Parameter file content Tom Joseph (Sat May 30 2009 - 21:23:48 CDT)
[AMBER] create a simulation box Workalemhu Berhanu (Sat May 30 2009 - 22:06:24 CDT)
- Re: [AMBER] create a simulation box Gustavo Seabra (Tue Jun 02 2009 - 10:08:46 CDT)
[AMBER] can I get partial charge for lipid membrane with Antechamber and RESP xueqin pang (Sun May 31 2009 - 07:43:09 CDT)
- Re: [AMBER] can I get partial charge for lipid membrane with Antechamber and RESP FyD (Sun May 31 2009 - 07:51:50 CDT)
[AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy xueqin pang (Sun May 31 2009 - 07:47:57 CDT)
- Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy Gustavo Seabra (Tue Jun 02 2009 - 09:53:19 CDT)
- Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy Marc Baaden (Tue Jun 02 2009 - 15:56:29 CDT)
  - Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy jacky zhao (Wed Jun 03 2009 - 08:44:12 CDT)
[AMBER] solutes in a simulation box Workalemhu Berhanu (Sun May 31 2009 - 11:59:39 CDT)
[AMBER] Choice of force feild manoj singh (Sun May 31 2009 - 12:12:23 CDT)
- Re: [AMBER] Choice of force feild Gustavo Seabra (Tue Jun 02 2009 - 09:58:11 CDT)
[AMBER] Choice of force field manoj singh (Sun May 31 2009 - 15:39:13 CDT)
- Re: [AMBER] Choice of force field Carlos Simmerling (Mon Jun 01 2009 - 06:14:09 CDT)
[AMBER] sleap and delete FyD (Mon Jun 01 2009 - 02:35:32 CDT)
[AMBER] converting vibrational frequency aneesh cna (Mon Jun 01 2009 - 06:22:01 CDT)
- Re: [AMBER] converting vibrational frequency David A. Case (Mon Jun 01 2009 - 06:39:32 CDT)
  - Re: [AMBER] converting vibrational frequency aneesh cna (Mon Jun 01 2009 - 11:53:22 CDT)
[AMBER] atom number exceeds the MAXATOM when running antechamber xueqin pang (Mon Jun 01 2009 - 07:53:23 CDT)
- Re: [AMBER] atom number exceeds the MAXATOM when running antechamber Gustavo Seabra (Tue Jun 02 2009 - 10:04:33 CDT)
[AMBER] different comformations to choose for RESP xueqin pang (Mon Jun 01 2009 - 08:47:30 CDT)
- Re: [AMBER] different comformations to choose for RESP FyD (Mon Jun 01 2009 - 09:32:21 CDT)
[AMBER] hbond_DNAtraj balaji nagarajan (Mon Jun 01 2009 - 12:08:15 CDT)
- Re: [AMBER] hbond_DNAtraj Jianyin Shao (Wed Jun 03 2009 - 11:52:41 CDT)
[AMBER] minimization to reduce covalent deviation Peter Varnai (Mon Jun 01 2009 - 15:25:07 CDT)
- Re: [AMBER] minimization to reduce covalent deviation David A. Case (Tue Jun 02 2009 - 08:38:58 CDT)
[AMBER] how to choose different comformations for RESP xueqin pang (Mon Jun 01 2009 - 19:32:51 CDT)
- Re: [AMBER] how to choose different comformations for RESP cgji (Tue Jun 02 2009 - 00:14:02 CDT)
[AMBER] MMPBSA and mm_pbsa_statistics.pl error john smith (Tue Jun 02 2009 - 00:38:54 CDT)
- Re: [AMBER] MMPBSA and mm_pbsa_statistics.pl error Ray Luo (Tue Jun 02 2009 - 23:49:34 CDT)
[AMBER] how to add ions bharat lakhani (Tue Jun 02 2009 - 02:25:46 CDT)
[AMBER] Atom names Rose Tamil (Tue Jun 02 2009 - 05:53:50 CDT)
- Re: [AMBER] Atom names Carlos Simmerling (Tue Jun 02 2009 - 06:39:25 CDT)
- Re: [AMBER] Atom names David A. Case (Tue Jun 02 2009 - 06:44:39 CDT)
  - Re: [AMBER] Atom names Rose Tamil (Tue Jun 02 2009 - 06:50:47 CDT)
[AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 07:46:14 CDT)
- Re: [AMBER] help with parameters for ions David A. Case (Tue Jun 02 2009 - 08:46:40 CDT)
  - Re: [AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 10:10:17 CDT)
    - Re: [AMBER] help with parameters for ions InSuk Joung (Tue Jun 02 2009 - 10:28:55 CDT)
  - Re: [AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 12:38:00 CDT)
    - Re: [AMBER] help with parameters for ions InSuk Joung (Tue Jun 02 2009 - 13:14:46 CDT)
[AMBER] Error in MM PBSA Vikas Sharma (Tue Jun 02 2009 - 08:42:16 CDT)
- Re: [AMBER] Error in MM PBSA David A. Case (Tue Jun 02 2009 - 09:05:09 CDT)
Fwd: Re: [AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 13:33:41 CDT)
[AMBER] PARMSCAN alegil_at_fq.uh.cu (Tue Jun 02 2009 - 17:26:42 CDT)
[AMBER] PARMSCAN alegil_at_fq.uh.cu (Tue Jun 02 2009 - 17:41:54 CDT)
[AMBER] preparation of two solutes of organic molecules in a simulation box Workalemhu Berhanu (Tue Jun 02 2009 - 18:09:04 CDT)
[AMBER] addions Shubhra Gupta (Wed Jun 03 2009 - 00:47:11 CDT)
- [AMBER] Re: addions Shubhra Gupta (Wed Jun 03 2009 - 06:12:32 CDT)
  - Re: [AMBER] Re: addions nicholus bhattacharjee (Wed Jun 03 2009 - 08:44:51 CDT)
  - [AMBER] Re: addions Peter Gannett (Wed Jun 03 2009 - 09:17:57 CDT)
    - Re: [AMBER] Re: addions Shubhra Gupta (Thu Jun 04 2009 - 23:38:20 CDT)
[AMBER] Distance restraints between groups of atoms Germain Vallverdu (Wed Jun 03 2009 - 01:58:57 CDT)
- Re: [AMBER] Distance restraints between groups of atoms David A. Case (Wed Jun 03 2009 - 07:27:04 CDT)
  - [AMBER] AMBER10: error message mdfil flag..... Catein Catherine (Wed Jun 03 2009 - 09:14:50 CDT)
    - Re: [AMBER] AMBER10: error message mdfil flag..... David A. Case (Wed Jun 03 2009 - 09:30:08 CDT)
  - Re: [AMBER] Distance restraints between groups of atoms Germain Vallverdu (Wed Jun 03 2009 - 09:43:37 CDT)
[AMBER] use of random seed in multiple runs Andrew Voronkov (Wed Jun 03 2009 - 04:28:52 CDT)
- Re: [AMBER] use of random seed in multiple runs Carlos Simmerling (Wed Jun 03 2009 - 05:13:23 CDT)
  - Re: [AMBER] use of random seed in multiple runs Andrew Voronkov (Wed Jun 03 2009 - 12:00:32 CDT)
- Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Wed Jun 03 2009 - 08:55:24 CDT)
- Re: [AMBER] use of random seed in multiple runs Andrew Voronkov (Wed Jun 03 2009 - 14:26:48 CDT)
  - Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Wed Jun 03 2009 - 21:00:51 CDT)
[AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov (Wed Jun 03 2009 - 05:28:15 CDT)
- Re: [AMBER] only ff94 and ff99 for GBSA? Carlos Simmerling (Wed Jun 03 2009 - 05:51:09 CDT)
- Re: [AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov (Wed Jun 03 2009 - 06:52:13 CDT)
  - Re: [AMBER] only ff94 and ff99 for GBSA? David A. Case (Wed Jun 03 2009 - 07:24:56 CDT)
[AMBER] NO output when running espgen? xueqin pang (Wed Jun 03 2009 - 08:13:06 CDT)
[AMBER] Pentavalent Phosphorous and Antechamber Peterson, Matthew W. (Wed Jun 03 2009 - 09:12:44 CDT)
- Re: [AMBER] Pentavalent Phosphorous and Antechamber David A. Case (Wed Jun 03 2009 - 11:35:26 CDT)
- Re: [AMBER] Pentavalent Phosphorous and Antechamber Shubhra Gupta (Wed Jun 03 2009 - 23:37:08 CDT)
- Re: [AMBER] Pentavalent Phosphorous and Antechamber FyD (Thu Jun 04 2009 - 01:29:59 CDT)
[AMBER] spc.itp for the Amber force field rebeca (Wed Jun 03 2009 - 09:46:46 CDT)
- Re: [AMBER] spc.itp for the Amber force field Alan (Wed Jun 03 2009 - 10:38:56 CDT)
[AMBER] problems with EP of TIP4PEW rebeca (Wed Jun 03 2009 - 10:43:58 CDT)
- Re: [AMBER] problems with EP of TIP4PEW David A. Case (Wed Jun 03 2009 - 11:29:43 CDT)
  - Re: [AMBER] problems with EP of TIP4PEW rebeca (Wed Jun 03 2009 - 13:40:12 CDT)
[AMBER] creating bond Jorgen Simonsen (Wed Jun 03 2009 - 12:04:11 CDT)
- Re: [AMBER] creating bond David A. Case (Wed Jun 03 2009 - 13:32:57 CDT)
- Re: [AMBER] creating bond Bill Ross (Wed Jun 03 2009 - 13:40:52 CDT)
  - Re: [AMBER] creating bond Jorgen Simonsen (Wed Jun 03 2009 - 14:56:29 CDT)
- Re: [AMBER] creating bond Bill Ross (Wed Jun 03 2009 - 16:40:09 CDT)
  - [AMBER] AMBER 10: sleap diff errors? Catein Catherine (Thu Jun 04 2009 - 00:37:35 CDT)
    - Re: [AMBER] AMBER 10: sleap diff errors? David A. Case (Thu Jun 04 2009 - 14:19:44 CDT)
[AMBER] ptraj image in non-orthorhombic cell Joanna Panecka (Wed Jun 03 2009 - 15:19:52 CDT)
[AMBER] bad atom type in mm_pbsa calculation. How to solve it? Thanks! Haizhen Zhong (Wed Jun 03 2009 - 18:00:34 CDT)
[AMBER] no output when running Antechamber(espgen) xueqin pang (Thu Jun 04 2009 - 01:02:32 CDT)
[AMBER] how to add water for membrane, in Z direction only or xyz xueqin pang (Thu Jun 04 2009 - 03:13:07 CDT)
[AMBER] Binding Energy Vikas Sharma (Thu Jun 04 2009 - 06:25:01 CDT)
[AMBER] Error in MM PBSA Vikas Sharma (Thu Jun 04 2009 - 09:58:43 CDT)
- Re: [AMBER] Error in MM PBSA Ray Luo (Thu Jun 04 2009 - 16:00:51 CDT)
- Re: [AMBER] Error in MM PBSA Vikas Sharma (Sat Jun 06 2009 - 04:03:22 CDT)
  - Re: [AMBER] Error in MM PBSA Ray Luo (Sat Jun 06 2009 - 09:37:43 CDT)
[AMBER] mol2 file to amber pdb file format balaji nagarajan (Thu Jun 04 2009 - 11:32:06 CDT)
- Re: [AMBER] mol2 file to amber pdb file format David A. Case (Thu Jun 04 2009 - 11:55:39 CDT)
[AMBER] rescaling velocities abi ghanem (Thu Jun 04 2009 - 11:39:02 CDT)
- Re: [AMBER] rescaling velocities Carlos Simmerling (Thu Jun 04 2009 - 11:43:20 CDT)
[AMBER] ptraj_hbond_problem balaji nagarajan (Thu Jun 04 2009 - 17:08:24 CDT)
- Re: [AMBER] ptraj_hbond_problem Thomas Cheatham (Fri Jun 05 2009 - 00:28:11 CDT)
[AMBER] Warning: No sp2 improper torsion term for Alan (Fri Jun 05 2009 - 07:26:55 CDT)
- RE: [AMBER] Warning: No sp2 improper torsion term for Ross Walker (Fri Jun 05 2009 - 09:13:53 CDT)
  - Re: [AMBER] Warning: No sp2 improper torsion term for Alan (Mon Jun 08 2009 - 09:54:50 CDT)
[AMBER] parameter for dihedral angle Jorgen Simonsen (Fri Jun 05 2009 - 10:16:56 CDT)
- Re: [AMBER] parameter for dihedral angle David A. Case (Fri Jun 05 2009 - 14:50:03 CDT)
- Re: [AMBER] parameter for dihedral angle raja pandian (Sat Jun 06 2009 - 00:13:52 CDT)
  - Re: [AMBER] parameter for dihedral angle David A. Case (Sat Jun 06 2009 - 07:47:35 CDT)
[AMBER] Proper ISTRNG value ? Marek Maly (Fri Jun 05 2009 - 11:24:58 CDT)
[AMBER] Computational Alanine Scanning using mm_pbsa, any tutorial for amber9 or amber 10 version? Haizhen Zhong (Fri Jun 05 2009 - 18:17:01 CDT)
[AMBER] average torsional energy Francesco Pietra (Sat Jun 06 2009 - 11:57:49 CDT)
- Re: [AMBER] average torsional energy Adrian Roitberg (Sun Jun 07 2009 - 11:09:14 CDT)
  - Re: [AMBER] average torsional energy Carlos Simmerling (Sun Jun 07 2009 - 11:14:17 CDT)
    - Re: [AMBER] average torsional energy Karl Kirschner (Mon Jun 08 2009 - 03:29:05 CDT)
    - Re: [AMBER] average torsional energy Francesco Pietra (Mon Jun 08 2009 - 04:11:52 CDT)
- [AMBER] Fwd: average torsional energy Francesco Pietra (Sun Jun 07 2009 - 11:09:37 CDT)
- [AMBER] How to calculate the distance of CA of all residues in the trajectory Thomas Leonard (Sun Jun 07 2009 - 20:45:54 CDT)
[AMBER] MaxRad ? Marek Maly (Sat Jun 06 2009 - 15:56:44 CDT)
[AMBER] POL3 Hemant Kumar (Sun Jun 07 2009 - 13:27:29 CDT)
[AMBER] vs_vikassharma@yahoo.co.in has sent you a private message Vikas S (Sun Jun 07 2009 - 14:28:00 CDT)
[AMBER] Max filename length in Sander? Paul Mortenson (Mon Jun 08 2009 - 05:59:52 CDT)
- Re: [AMBER] Max filename length in Sander? David A. Case (Mon Jun 08 2009 - 07:28:41 CDT)
  - Re: [AMBER] Max filename length in Sander? Robert Duke (Mon Jun 08 2009 - 12:30:47 CDT)
    - RE: [AMBER] Max filename length in Sander? Paul Mortenson (Tue Jun 09 2009 - 09:47:57 CDT)
    - Re: [AMBER] Max filename length in Sander? Robert Duke (Tue Jun 09 2009 - 10:01:39 CDT)
- Re: [AMBER] Max filename length in Sander? David A. Case (Mon Jun 08 2009 - 07:36:32 CDT)
[AMBER] (no subject) Vishal Maingi (Mon Jun 08 2009 - 06:14:22 CDT)
- Re: [AMBER] (no subject) Karl Kirschner (Mon Jun 08 2009 - 06:38:42 CDT)
- Re: [AMBER] (no subject) FyD (Mon Jun 08 2009 - 12:14:05 CDT)
[AMBER] Lost mail Robert Duke (Mon Jun 08 2009 - 06:58:02 CDT)
[AMBER] problem with creation of prmtop and prmcrd files moitrayee_at_mbu.iisc.ernet.in (Mon Jun 08 2009 - 08:00:18 CDT)
- Re: [AMBER] problem with creation of prmtop and prmcrd files Tom Joseph (Wed Jun 10 2009 - 20:30:19 CDT)
[AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files] moitrayee_at_mbu.iisc.ernet.in (Mon Jun 08 2009 - 09:28:14 CDT)
[AMBER] sander error Beale, John (Mon Jun 08 2009 - 09:43:24 CDT)
- RE: [AMBER] sander error Ross Walker (Mon Jun 08 2009 - 20:41:06 CDT)
  - Re: [AMBER] sander error Robert Duke (Mon Jun 08 2009 - 22:27:52 CDT)
[AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files]] moitrayee_at_mbu.iisc.ernet.in (Mon Jun 08 2009 - 09:30:21 CDT)
[AMBER] Unknown residue: MOL number: 30 type: Terminal/last Workalemhu Berhanu (Mon Jun 08 2009 - 13:30:43 CDT)
- Re: [AMBER] Unknown residue: MOL number: 30 type: Terminal/last David A. Case (Tue Jun 09 2009 - 06:51:42 CDT)
[AMBER] mm_pbsa_statistics-CALC DELTA parameter ? Marek Maly (Mon Jun 08 2009 - 14:16:19 CDT)
[AMBER] Strange contacts with water molecules Jordan MONNET (Mon Jun 08 2009 - 16:39:26 CDT)
- RE: [AMBER] Strange contacts with water molecules Ross Walker (Mon Jun 08 2009 - 22:16:41 CDT)
  - Re: [AMBER] Strange contacts with water molecules Jordan MONNET (Tue Jun 09 2009 - 11:01:53 CDT)
    - Re: [AMBER] Strange contacts with water molecules Jordan MONNET (Wed Jun 17 2009 - 12:00:46 CDT)
[AMBER] Error in MM PBSA (vertex atom mismatch) Vikas Sharma (Tue Jun 09 2009 - 01:33:38 CDT)
[AMBER] ptraj quasiharmonic analysis Neha Gandhi (Tue Jun 09 2009 - 01:38:01 CDT)
- Re: [AMBER] ptraj quasiharmonic analysis Hannes Loeffler (Tue Jun 09 2009 - 02:19:23 CDT)
[AMBER] (no subject) david.lisgarten_at_canterbury.ac.uk (Tue Jun 09 2009 - 05:23:57 CDT)
- Re: [AMBER] (no subject) David A. Case (Tue Jun 09 2009 - 06:47:59 CDT)
  - RE: [AMBER] (no subject) david.lisgarten_at_canterbury.ac.uk (Tue Jun 09 2009 - 08:56:32 CDT)
    - RE: [AMBER] (no subject) david.lisgarten_at_canterbury.ac.uk (Thu Jun 11 2009 - 03:28:56 CDT)
    - Re: [AMBER] (no subject) David A. Case (Thu Jun 11 2009 - 06:54:38 CDT)
[AMBER] SOS - too high binding energy Marek Maly (Tue Jun 09 2009 - 05:49:43 CDT)
- Re: [AMBER] SOS - too high binding energy Marek Maly (Wed Jun 10 2009 - 14:47:58 CDT)
[AMBER] unit of charge in prep files moitrayee_at_mbu.iisc.ernet.in (Tue Jun 09 2009 - 06:35:51 CDT)
- Re: [AMBER] unit of charge in prep files David A. Case (Tue Jun 09 2009 - 08:07:08 CDT)
  - Re: [AMBER] unit of charge in prep files moitrayee_at_mbu.iisc.ernet.in (Tue Jun 09 2009 - 20:18:58 CDT)
[AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script Samuel Genheden (Tue Jun 09 2009 - 07:43:19 CDT)
- Re: [AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script David A. Case (Tue Jun 09 2009 - 08:20:22 CDT)
[AMBER] Vertex atom mismatch in Amber Vikas Sharma (Tue Jun 09 2009 - 08:41:33 CDT)
[AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 09:30:39 CDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling (Tue Jun 09 2009 - 09:38:14 CDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 10:33:51 CDT)
  - Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling (Tue Jun 09 2009 - 10:36:50 CDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 10:44:39 CDT)
  - RE: [AMBER] DNA as well as protein distorted during MD run in sander Jesse Dylan Ziebarth (jziebrth) (Tue Jun 09 2009 - 10:47:34 CDT)
  - Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling (Tue Jun 09 2009 - 10:48:30 CDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 11:02:56 CDT)
[AMBER] Improper dihedrals between residues? Ben Roberts (Tue Jun 09 2009 - 11:11:15 CDT)
- Re: [AMBER] Improper dihedrals between residues? Carlos Simmerling (Tue Jun 09 2009 - 11:28:04 CDT)
  - Re: [AMBER] Improper dihedrals between residues? David A. Case (Tue Jun 09 2009 - 12:14:57 CDT)
    - Re: [AMBER] Improper dihedrals between residues? Carlos Simmerling (Tue Jun 09 2009 - 12:51:40 CDT)
- Re: [AMBER] Improper dihedrals between residues? Bill Ross (Tue Jun 09 2009 - 16:17:03 CDT)
  - [AMBER] radial distribution without normalization CHAMI F. (Wed Jun 10 2009 - 10:48:12 CDT)
    - Re: [AMBER] radial distribution without normalization Thomas Cheatham (Wed Jun 10 2009 - 17:11:40 CDT)
Re: [AMBER] Improper dihedrals between residues? Bill Ross (Tue Jun 09 2009 - 14:04:02 CDT)
- Re: [AMBER] Improper dihedrals between residues? Ben Roberts (Tue Jun 09 2009 - 14:12:07 CDT)
[AMBER] POL3 & SHAKE Hemant Gangwar (Tue Jun 09 2009 - 15:53:27 CDT)
- Re: [AMBER] POL3 & SHAKE David A. Case (Wed Jun 10 2009 - 14:11:40 CDT)
[AMBER] MM PBSA ( Vertex atom mismatch in Amber) Vikas Sharma (Tue Jun 09 2009 - 22:28:22 CDT)
[AMBER] GAFF and solvents.lib error Vishal Maingi (Wed Jun 10 2009 - 05:25:38 CDT)
- Re: [AMBER] GAFF and solvents.lib error David A. Case (Wed Jun 10 2009 - 10:54:05 CDT)
[AMBER] Thermodynamic parameters in mm_PBSA - NAB ? Marek Maly (Wed Jun 10 2009 - 05:33:59 CDT)
- Re: [AMBER] Thermodynamic parameters in mm_PBSA - NAB ? Dav