AMBER Archive (2009) - May 2009 By Thread

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Starting: Fri May 01 2009 - 03:33:34 CDT
Ending: Sun May 31 2009 - 15:39:13 CDT

[AMBER] ongoing issues using sander with AMOEBA Tomasio, Susana (Wed May 13 2009 - 05:00:00 CDT)

Re: [AMBER] pmemd compilation error john smith (Tue May 05 2009 - 06:20:08 CDT)

Re: [AMBER] chain restrain x TI Josmar R. da Rocha (Sat May 02 2009 - 12:09:53 CDT)

Re: [AMBER] Amber FF and Glycam Hannes Loeffler (Fri May 01 2009 - 03:33:34 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 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)
[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)
[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)
[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)
[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)
[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)
[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)
[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)
[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)
[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)
[AMBER] Choice of force field manoj singh (Sun May 31 2009 - 15:39:13 CDT)
- RE: [AMBER] QM/MM Syed Tarique Moin (Mon May 04 2009 - 17:13:22 CDT)
  - RE: [AMBER] QM/MM Ross Walker (Tue May 05 2009 - 17:16:26 CDT)
- RE: [AMBER] QM/MM Syed Tarique Moin (Wed May 06 2009 - 02:11:54 CDT)
- RE: [AMBER] QM/MM Syed Tarique Moin (Wed May 06 2009 - 02:12:17 CDT)

Last message date: Thu Dec 31 2009 - 22:57:46 CST
Archived on: Thu Dec 31 2009 - 22:58:32 CST

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