AMBER Archive (2005) - May 2005 By ThreadMost recent messages
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Starting: Sun May 01 2005 - 16:00:59 CDT
Ending: Tue May 31 2005 - 22:41:42 CDT
- AMBER: Identifying water molecules with ptraj Joseph Fernandez (Sun May 01 2005 - 16:00:59 CDT)
- AMBER: fast 1/r methods Brent Krueger (Mon May 02 2005 - 06:51:56 CDT)
- AMBER: How to fix the atom in NPT case? george Chen (Mon May 02 2005 - 13:19:54 CDT)
- AMBER: sander run YoungJin Cho (Mon May 02 2005 - 15:45:01 CDT)
- AMBER: GB with dipoles ! Pradipta Bandyopadhyay (Tue May 03 2005 - 06:54:44 CDT)
- Fwd: Re: AMBER: AMBER Test Anthony Cruz (Tue May 03 2005 - 07:25:46 CDT)
- AMBER: Can I add iodide anione? Myunggi Yi (Tue May 03 2005 - 12:36:07 CDT)
- AMBER: rborn(i) in egb.f Harianto Tjong (Tue May 03 2005 - 14:04:39 CDT)
- AMBER: NOE constraints Hui-Hsu Tsai (Tue May 03 2005 - 14:18:27 CDT)
- AMBER: Relative stability with MMPBSA Angelo Pugliese (Wed May 04 2005 - 11:09:27 CDT)
- AMBER: Bromelain PDF xleap load error Thomas Patko (Wed May 04 2005 - 12:13:35 CDT)
- AMBER: mm/pbsa error Eric Hu (Wed May 04 2005 - 13:06:34 CDT)
- AMBER: Meaning of induced dipole moments for atom pairs? Cenk Andac (Wed May 04 2005 - 15:52:06 CDT)
- AMBER: How can I read parm99.dat file? Myunggi Yi (Wed May 04 2005 - 18:08:49 CDT)
- Re: AMBER: How can I read parm99.dat file? Bill Ross (Wed May 04 2005 - 19:12:08 CDT)
- AMBER: ibelly in nmode Dawei Zhang (Thu May 05 2005 - 14:23:13 CDT)
- AMBER: problem with gb md emilia wu (Thu May 05 2005 - 21:05:00 CDT)
- AMBER: No vdW parameters for HO.. Vineet Pande (Fri May 06 2005 - 05:20:02 CDT)
- AMBER: a nomenclature question Kenley Barrett (Fri May 06 2005 - 11:11:24 CDT)
- AMBER: Dr. Cornell's calculation of Sulfur vdw epsilon value in parm94.dat? Chris Moth (Fri May 06 2005 - 14:32:23 CDT)
- 75% Off for All New Softs Now! haberman Rogelio Adams (Fri May 06 2005 - 22:19:57 CDT)
- AMBER: langevin, GB and simulated annealing - 5 pascal.baillod_at_epfl.ch (Mon May 09 2005 - 11:25:12 CDT)
- AMBER: radial distribution function Myunggi Yi (Mon May 09 2005 - 13:36:43 CDT)
- The new ganaration of repliccas is here capella Linda Hooks (Mon May 09 2005 - 20:53:45 CDT)
- AMBER: parameter for sulfur in thio-octyl-glucopyranoside Vijay Manickam Achari (Mon May 09 2005 - 22:23:07 CDT)
- AMBER: AMBER8 Build on Linux x64 running Opterons Thomas Patko (Wed May 11 2005 - 02:10:14 CDT)
- AMBER: Trouble with example tutorial Maciej (Wed May 11 2005 - 06:08:02 CDT)
- You wont believe these pr1ces on name-brannd soft's! kerchief Ismael Childers (Wed May 11 2005 - 10:06:11 CDT)
- AMBER: Parameter for alpha-lactose Sagarika Dev (Wed May 11 2005 - 09:48:21 CDT)
- AMBER: Asking how to creat alanine "dipeptide" in amber8 Li Su (Wed May 11 2005 - 10:37:07 CDT)
- Fwd: Re: AMBER: AMBER Test Anthony Cruz (Wed May 11 2005 - 10:49:38 CDT)
- AMBER: SANDER BOMB: volume of ucell too big Stern, Julie (Wed May 11 2005 - 11:07:38 CDT)
- AMBER: maximum number of processors MURAT CETINKAYA (Wed May 11 2005 - 22:53:44 CDT)
- We can send you disccounted errection mads party Freeman William (Thu May 12 2005 - 00:23:35 CDT)
- AMBER: RESP charge fitting for N-methylguanine cation Grzegorz Jezierski (Thu May 12 2005 - 11:50:17 CDT)
- AMBER: Tutorial #1 ptraj/sander problem Daniela Kohen (Thu May 12 2005 - 17:03:07 CDT)
- AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang (Thu May 12 2005 - 20:44:04 CDT)
- AMBER: amber8 test error Cordova, Luis E. (Thu May 12 2005 - 22:26:00 CDT)
- AMBER: creating residues - charge assign problems Hayden Eastwood (Fri May 13 2005 - 06:06:06 CDT)
- AMBER: platinum atom in Xleap Chen Chengwen (Fri May 13 2005 - 21:11:12 CDT)
- AMBER: How to create a parallel job for amber 8? Ò׺ç (Sat May 14 2005 - 06:20:15 CDT)
- A new rollax repliccas is in the mark. attitudinal Russel Granger (Sat May 14 2005 - 11:02:36 CDT)
- AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? caoch_at_cherry.bio.titech.ac.jp (Sat May 14 2005 - 12:17:17 CDT)
- AMBER: Calculating of radius of gyration in Carnal Hwankyu Lee (Sat May 14 2005 - 13:36:37 CDT)
- Re: AMBER: Calculating of radius of gyration in Carnal Bill Ross (Sat May 14 2005 - 17:26:43 CDT)
- AMBER: how to reduce box size and delete excess solvent hj zou (Sun May 15 2005 - 06:51:32 CDT)
- AMBER: How to set constraint Li Su (Sun May 15 2005 - 13:58:51 CDT)
- Re: AMBER: how to reduce box size and delete excess solvent Bill Ross (Sun May 15 2005 - 14:50:01 CDT)
- AMBER: generating over 16 bps of DNA in nucgen Hwankyu Lee (Mon May 16 2005 - 10:33:04 CDT)
- AMBER: strange mm_pbsa.pl bug Nelson Fonseca (Mon May 16 2005 - 10:39:21 CDT)
- AMBER: How to set up dihedral constraints in amber Li Su (Mon May 16 2005 - 10:39:50 CDT)
- AMBER: output of force field info Stern, Julie (Mon May 16 2005 - 14:24:37 CDT)
- AMBER: nmode in mmpbsa Joseph Fernandez (Mon May 16 2005 - 18:36:28 CDT)
- AMBER: MMPBSA calculations on Highly charged systems Vitor Manuel Sousa F?x (Tue May 17 2005 - 06:01:21 CDT)
- AMBER: Message in .out file Atilio Anzellotti (Tue May 17 2005 - 07:31:36 CDT)
- AMBER: GAFF angle parameters Monica Civera (Tue May 17 2005 - 11:11:46 CDT)
- AMBER: compiling pmemd on dual xeon Tiziano Tuccinardi (Tue May 17 2005 - 12:28:31 CDT)
- AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Rajeev Ranjan Singh (Tue May 17 2005 - 15:15:33 CDT)
- FW: Office XP - 60 dolars! coagulate Myra Cole (Tue May 17 2005 - 19:04:52 CDT)
- AMBER: RE: Tutorial#1 ptraj/sander problem Ross Walker (Tue May 17 2005 - 17:56:59 CDT)
- AMBER: MD on surface Yanze Zhang (Tue May 17 2005 - 18:58:29 CDT)
- AMBER: error with ptraj Xiaowei (David) Li (Tue May 17 2005 - 23:27:33 CDT)
- AMBER: loading pdb cbala_at_igib.res.in (Wed May 18 2005 - 00:56:13 CDT)
- AMBER: Using AMBER for Carbon nanotubes Zhang Yingyan (Wed May 18 2005 - 03:21:42 CDT)
- AMBER: error during MD run cbala_at_igib.res.in (Wed May 18 2005 - 13:39:25 CDT)
- AMBER: frcmod info for Nickel Kara Di Giorgio (Wed May 18 2005 - 14:04:44 CDT)
- AMBER: parameter for sulfur in thio-glucoside residue Vijay Manickam Achari (Wed May 18 2005 - 20:58:57 CDT)
- AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim (Wed May 18 2005 - 21:16:35 CDT)
- AMBER: Amber 8 and LAM compilation problem Glen Otero (Thu May 19 2005 - 00:52:00 CDT)
- AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Vijay Manickam Achari (Thu May 19 2005 - 01:55:21 CDT)
- AMBER: GB - igb=1 versus dielc=? milion_at_c-box.cz (Thu May 19 2005 - 03:36:34 CDT)
- AMBER: write format of restart crd in sander/pmemd Peter Varnai (Thu May 19 2005 - 07:12:22 CDT)
- AMBER: Using amber4 generated prep files in amber8? Simon Whitehead (Thu May 19 2005 - 07:51:00 CDT)
- AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 20:19:04 CDT)
- AMBER: MM_PBSA for NMR restrained structures Cenk Andac (Fri May 20 2005 - 03:36:10 CDT)
- AMBER: leap problem: savepdb Hannes Barsch (Fri May 20 2005 - 04:30:29 CDT)
- AMBER: how to creat leaprc.gaff Vijay Manickam Achari (Fri May 20 2005 - 04:36:25 CDT)
- AMBER: Error in minimization Priti Hansia (Fri May 20 2005 - 05:58:36 CDT)
- Re: AMBER: Representation of cations in MD David A. Case (Fri May 20 2005 - 10:16:15 CDT)
- AMBER: Steve Seibold (Fri May 20 2005 - 12:45:24 CDT)
- AMBER: crashing xleap Kenley Barrett (Fri May 20 2005 - 13:48:13 CDT)
- AMBER: 1-4 scaling factors Stern, Julie (Fri May 20 2005 - 14:13:22 CDT)
- Re: AMBER: crashing xleap Bill Ross (Fri May 20 2005 - 14:55:15 CDT)
- AMBER: Citing the PBSA module of AMBER8 Cenk Andac (Fri May 20 2005 - 16:27:03 CDT)
- AMBER: modeller Zhang Bing (Fri May 20 2005 - 23:53:13 CDT)
- AMBER: rotating and repositioning molecules in xleap Hwankyu Lee (Sat May 21 2005 - 01:09:45 CDT)
- AMBER: Copyright for PBSA Cenk Andac (Sat May 21 2005 - 03:32:00 CDT)
- AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Sun May 22 2005 - 14:44:55 CDT)
- Re: AMBER: Unexpected stop of Sander run Bill Ross (Sun May 22 2005 - 15:18:16 CDT)
- AMBER: Error in sander: stack trace terminated abnormally. Hwankyu Lee (Sun May 22 2005 - 16:05:31 CDT)
- AMBER: antechamber not working .. for thio residue.. Vijay Manickam Achari (Sun May 22 2005 - 21:15:20 CDT)
- AMBER: Setting Amber force field parameters Chen Chengwen (Mon May 23 2005 - 02:55:38 CDT)
- AMBER: using antechamber ... to get prepin file Vijay Manickam Achari (Mon May 23 2005 - 03:59:16 CDT)
- AMBER: Connecting two molecules Hwankyu Lee (Mon May 23 2005 - 10:13:00 CDT)
- AMBER: how to generate frcmod file for using prepin file.. Vijay Manickam Achari (Mon May 23 2005 - 21:52:18 CDT)
- AMBER: my frcmod file created using parmchk Vijay Manickam Achari (Mon May 23 2005 - 22:44:21 CDT)
- AMBER: my prepin file in lowe-case Vijay Manickam Achari (Tue May 24 2005 - 02:51:55 CDT)
- AMBER: Which forcefield? Simon Whitehead (Tue May 24 2005 - 03:13:01 CDT)
- AMBER: conformational sampling of a peptide Hannes Barsch (Tue May 24 2005 - 03:58:04 CDT)
- AMBER: amber code Juan Fernandez Carmona (Tue May 24 2005 - 05:08:00 CDT)
- Re: AMBER: conformational sampling of a peptide Carlos Simmerling (Tue May 24 2005 - 08:11:53 CDT)
- AMBER: Fw: Installing PMEMD on IBM machine (CPU power4) running SUSE_9.1 Robert Duke (Tue May 24 2005 - 09:42:15 CDT)
- AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_' René Ranzinger (Tue May 24 2005 - 10:04:42 CDT)
- AMBER: Sander Restart Problem Garhan Attebury (Tue May 24 2005 - 10:07:49 CDT)
- AMBER: How to fix certain bond angles Li Su (Tue May 24 2005 - 10:27:14 CDT)
- AMBER: Error: vlimit exceeded for step Hwankyu Lee (Tue May 24 2005 - 12:20:10 CDT)
- Solute-solvent boundary in pbsa ..Re: AMBER: Copyright for PBSA Cenk Andac (Tue May 24 2005 - 13:48:26 CDT)
- AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Li Su (Tue May 24 2005 - 14:14:09 CDT)
- AMBER: charges difference of atom in xleap and prmtop chaiann ng (Tue May 24 2005 - 23:02:33 CDT)
- AMBER: PARMSCAN program Philippe ARNAUD (Wed May 25 2005 - 02:28:31 CDT)
- AMBER: average structure after MD kuljeets_at_igib.res.in (Wed May 25 2005 - 04:14:19 CDT)
- AMBER: quadrupole in resp riccardo nifosi (Wed May 25 2005 - 05:44:20 CDT)
- AMBER: error in chirality.c? Kenley Barrett (Wed May 25 2005 - 09:27:07 CDT)
- Re#2:Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac (Wed May 25 2005 - 15:03:47 CDT)
- AMBER: dissolving micelle structure in water.. amber7 Vijay Manickam Achari (Wed May 25 2005 - 22:59:22 CDT)
- AMBER: distance restraints between two centers of mass JAVIER PEREZ (Thu May 26 2005 - 03:37:30 CDT)
- AMBER: Is the MD simulation normal Shulin Zhuang (Thu May 26 2005 - 10:30:48 CDT)
- AMBER: setting up Parallel processing mathew k varghese (Thu May 26 2005 - 10:39:00 CDT)
- AMBER: hbond analysis in ptaj/carnal Jana Precechtelova (Thu May 26 2005 - 11:25:20 CDT)
- Re: AMBER: hbond analysis in ptaj/carnal Bill Ross (Thu May 26 2005 - 11:44:13 CDT)
- AMBER: why is snaupe.f is empty? Cordova, Luis E. (Thu May 26 2005 - 12:06:24 CDT)
- AMBER: ptraj - hbond detailed analysis over time? pascal.baillod_at_epfl.ch (Thu May 26 2005 - 12:38:38 CDT)
- AMBER: Mol2 to prepin file conversion Andrew Box (Thu May 26 2005 - 19:08:22 CDT)
- AMBER: question about loadiing pdb file of a molecule complex gtg549i_at_mail.gatech.edu (Fri May 27 2005 - 16:39:28 CDT)
- AMBER: Workshop Tutorials Downtime this weekend. Ross Walker (Fri May 27 2005 - 16:49:05 CDT)
- AMBER: Antechamber RESP failed for large organic molecule junwang (Sun May 29 2005 - 14:57:59 CDT)
- AMBER: question about initial conditions for amber Ed Pate (Sun May 29 2005 - 21:42:21 CDT)
- AMBER: density profiles in ptraj or carnal Hwankyu Lee (Sun May 29 2005 - 22:27:37 CDT)
- AMBER: pairwise energy decomposition using MM-PBSA Xin Hu (Sun May 29 2005 - 22:38:30 CDT)
- AMBER: Force field modification problem yuann (Mon May 30 2005 - 06:16:27 CDT)
- AMBER: Bond angle restraints setting files Li Su (Mon May 30 2005 - 11:05:15 CDT)
- Re: AMBER: density profiles in ptraj or carnal Bill Ross (Mon May 30 2005 - 12:00:08 CDT)
- AMBER: density problem cristian obiol (Tue May 31 2005 - 04:17:46 CDT)
- AMBER: stack terminated abnormally drugdesign (Tue May 31 2005 - 05:20:33 CDT)
- AMBER: if setting ntf=4, will it cause someproblem? Li Su (Tue May 31 2005 - 09:55:03 CDT)
- AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Tue May 31 2005 - 10:23:51 CDT)
- AMBER: DNA base-flipping: TI vs PMF Lauren O'Neil (Tue May 31 2005 - 10:40:45 CDT)
- AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Grzegorz Jezierski (Tue May 31 2005 - 11:04:20 CDT)
- AMBER: MM-PBSA calculation masi_at_nmr.mpibpc.mpg.de (Tue May 31 2005 - 11:37:40 CDT)
- AMBER: STOP 0 masi_at_nmr.mpibpc.mpg.de (Tue May 31 2005 - 11:40:25 CDT)
- AMBER:Sander errors: Unit 6 Error on OPEN: mdout Douali, Latifa (Tue May 31 2005 - 12:34:41 CDT)
- Re: AMBER: STOP 0 Bill Ross (Tue May 31 2005 - 12:43:32 CDT)
- AMBER: meaningful tax for sander question Cordova, Luis E. (Tue May 31 2005 - 14:19:30 CDT)
- AMBER: double counting of potentials Stern, Julie (Tue May 31 2005 - 18:04:43 CDT)
- AMBER: Working with a nickel-organometallic compound Kara Di Giorgio (Tue May 31 2005 - 18:36:30 CDT)
- AMBER: External Field in AMBER? junwang (Tue May 31 2005 - 21:19:38 CDT)
Last message date: Sat Dec 31 2005 - 12:51:27 CST
Archived on: Sat Dec 31 2005 - 12:51:45 CST
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