Amber Archive May 2005: By Thread

AMBER: Identifying water molecules with ptraj Joseph Fernandez (Sun May 01 2005 - 14:00:59 PDT)
AMBER: fast 1/r methods Brent Krueger (Mon May 02 2005 - 04:51:56 PDT)
- Re: AMBER: fast 1/r methods fangyu liang (Mon May 02 2005 - 07:17:32 PDT)
- Re: AMBER: fast 1/r methods Andreas Svrcek-Seiler (Mon May 02 2005 - 07:18:22 PDT)
Re: AMBER: ipol=1 & use_pme= ?? David A. Case (Mon May 02 2005 - 09:44:47 PDT)
AMBER: How to fix the atom in NPT case? george Chen (Mon May 02 2005 - 11:19:54 PDT)
- Re: AMBER: How to fix the atom in NPT case? David A. Case (Mon May 02 2005 - 11:31:26 PDT)
  - Re: AMBER: How to fix the atom in NPT case? george Chen (Mon May 02 2005 - 12:35:42 PDT)
  - Re: AMBER: How to fix the atom in NPT case? george Chen (Tue May 03 2005 - 13:50:59 PDT)
    - Re: AMBER: How to fix the atom in NPT case? David A. Case (Tue May 03 2005 - 17:16:33 PDT)
Re: AMBER: Re: R.E.D. question Yanze Zhang (Mon May 02 2005 - 12:19:14 PDT)
- Re: AMBER: Re: R.E.D. question FyD (Mon May 02 2005 - 12:53:35 PDT)
AMBER: sander run YoungJin Cho (Mon May 02 2005 - 13:45:01 PDT)
AMBER: GB with dipoles ! Pradipta Bandyopadhyay (Tue May 03 2005 - 04:54:44 PDT)
Fwd: Re: AMBER: AMBER Test Anthony Cruz (Tue May 03 2005 - 05:25:46 PDT)
AMBER: Can I add iodide anione? Myunggi Yi (Tue May 03 2005 - 10:36:07 PDT)
AMBER: rborn(i) in egb.f Harianto Tjong (Tue May 03 2005 - 12:04:39 PDT)
- Re: AMBER: rborn(i) in egb.f John Mongan (Tue May 03 2005 - 11:26:15 PDT)
  - Re: AMBER: rborn(i) in egb.f Harianto Tjong (Tue May 03 2005 - 13:31:43 PDT)
    - Re: AMBER: rborn(i) in egb.f David A. Case (Tue May 03 2005 - 13:23:14 PDT)
    - Re: AMBER: rborn(i) in egb.f Harianto Tjong (Tue May 03 2005 - 15:13:16 PDT)
    - Re: AMBER: rborn(i) in egb.f David A. Case (Tue May 03 2005 - 15:59:23 PDT)
AMBER: NOE constraints Hui-Hsu Tsai (Tue May 03 2005 - 12:18:27 PDT)
- Re: AMBER: NOE constraints David A. Case (Tue May 03 2005 - 13:25:44 PDT)
AMBER: Relative stability with MMPBSA Angelo Pugliese (Wed May 04 2005 - 09:09:27 PDT)
AMBER: Bromelain PDF xleap load error Thomas Patko (Wed May 04 2005 - 10:13:35 PDT)
- Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) Thomas Patko (Thu May 05 2005 - 15:02:40 PDT)
  - Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) JunJun Liu (Thu May 05 2005 - 17:37:36 PDT)
  - Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) Andy Purkiss (Fri May 06 2005 - 04:05:36 PDT)
    - Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) Thomas Patko (Wed May 11 2005 - 00:10:53 PDT)
AMBER: mm/pbsa error Eric Hu (Wed May 04 2005 - 11:06:34 PDT)
- Re: AMBER: mm/pbsa error Scott Pendley (Tue May 10 2005 - 12:56:52 PDT)
AMBER: Meaning of induced dipole moments for atom pairs? Cenk Andac (Wed May 04 2005 - 13:52:06 PDT)
- Re: AMBER: Meaning of induced dipole moments for atom pairs? David A. Case (Wed May 04 2005 - 15:13:14 PDT)
- Re: AMBER: Meaning of induced dipole moments for atom pairs? Cenk Andac (Thu May 05 2005 - 17:28:49 PDT)
  - AMBER: keeping two domains closed together during a simulation Sergio E. Wong (Thu May 05 2005 - 17:44:45 PDT)
AMBER: How can I read parm99.dat file? Myunggi Yi (Wed May 04 2005 - 16:08:49 PDT)
- Re: AMBER: How can I read parm99.dat file? David A. Case (Thu May 05 2005 - 08:10:59 PDT)
  - Re: AMBER: How can I read parm99.dat file? Myunggi Yi (Fri May 06 2005 - 06:18:47 PDT)
- Re: AMBER: How can I read parm99.dat file? Bill Ross (Fri May 06 2005 - 13:08:59 PDT)
Re: AMBER: How can I read parm99.dat file? Bill Ross (Wed May 04 2005 - 17:12:08 PDT)
- Re: AMBER: How can I read parm99.dat file? Vineet Pande (Thu May 05 2005 - 02:12:09 PDT)
- Re: AMBER: How can I read parm99.dat file? Myunggi Yi (Fri May 06 2005 - 07:14:04 PDT)
- Re: AMBER: How can I read parm99.dat file? Myunggi Yi (Fri May 06 2005 - 07:14:15 PDT)
AMBER: ibelly in nmode Dawei Zhang (Thu May 05 2005 - 12:23:13 PDT)
- Re: AMBER: ibelly in nmode David A. Case (Sat May 07 2005 - 09:44:21 PDT)
AMBER: problem with gb md emilia wu (Thu May 05 2005 - 19:05:00 PDT)
- RE: AMBER: problem with gb md Ross Walker (Thu May 05 2005 - 21:47:40 PDT)
  - Re: RE: AMBER: problem with gb md emilia wu (Thu May 05 2005 - 23:29:33 PDT)
    - Re: RE: AMBER: problem with gb md Andreas Svrcek-Seiler (Fri May 06 2005 - 02:19:00 PDT)
AMBER: No vdW parameters for HO.. Vineet Pande (Fri May 06 2005 - 03:20:02 PDT)
- Re: AMBER: No vdW parameters for HO.. David A. Case (Fri May 06 2005 - 07:38:16 PDT)
  - Re: AMBER: No vdW parameters for HO.. Vineet Pande (Fri May 06 2005 - 08:40:09 PDT)
    - Re: AMBER: No vdW parameters for HO.. Yong Duan (Fri May 06 2005 - 09:28:25 PDT)
AMBER: a nomenclature question Kenley Barrett (Fri May 06 2005 - 09:11:24 PDT)
- Re: AMBER: a nomenclature question David A. Case (Thu May 12 2005 - 15:18:20 PDT)
AMBER: Dr. Cornell's calculation of Sulfur vdw epsilon value in parm94.dat? Chris Moth (Fri May 06 2005 - 12:32:23 PDT)
AMBER: langevin, GB and simulated annealing - 5 pascal.baillod.epfl.ch (Mon May 09 2005 - 09:25:12 PDT)
- Re: AMBER: langevin, GB and simulated annealing - 5 Carlos Simmerling (Mon May 09 2005 - 12:58:57 PDT)
  - Re: AMBER: langevin, GB and simulated annealing - 5 Carlos Simmerling (Tue May 10 2005 - 04:58:42 PDT)
  - AMBER: Problem with xleap Ilyas Yildirim (Wed May 11 2005 - 18:45:50 PDT)
    - Re: AMBER: Problem with xleap FyD (Wed May 11 2005 - 19:21:12 PDT)
    - Re: AMBER: Problem with xleap Ilyas Yildirim (Thu May 12 2005 - 16:14:38 PDT)
    - Re: AMBER: Problem with xleap JunJun Liu (Thu May 12 2005 - 00:19:24 PDT)
- Re: AMBER: langevin, GB and simulated annealing - 5 David A. Case (Mon May 09 2005 - 16:18:04 PDT)
AMBER: radial distribution function Myunggi Yi (Mon May 09 2005 - 11:36:43 PDT)
AMBER: parameter for sulfur in thio-octyl-glucopyranoside Vijay Manickam Achari (Mon May 09 2005 - 20:23:07 PDT)
- RE: AMBER: parameter for sulfur in thio-octyl-glucopyranoside Spero Manolatos (Thu May 12 2005 - 15:08:49 PDT)
Re: AMBER: radius parameter for F atom Scott Pendley (Tue May 10 2005 - 12:49:21 PDT)
AMBER: AMBER8 Build on Linux x64 running Opterons Thomas Patko (Wed May 11 2005 - 00:10:14 PDT)
- Re: AMBER: AMBER8 Build on Linux x64 running Opterons Mark Rance (Wed May 11 2005 - 08:02:05 PDT)
  - Re: AMBER: AMBER8 Build on Linux x64 running Opterons Robert Duke (Wed May 11 2005 - 08:14:50 PDT)
    - Re: AMBER: AMBER8 Build on Linux x64 running Opterons Robert Duke (Wed May 11 2005 - 08:18:12 PDT)
    - Re: AMBER: AMBER8 Build on Linux x64 running Opterons Thomas Patko (Wed May 11 2005 - 08:34:18 PDT)
  - Re: AMBER: AMBER8 Build on Linux x64 running Opterons David A. Case (Thu May 12 2005 - 09:58:19 PDT)
- Re: AMBER: AMBER8 Build on Linux x64 running Opterons Bill Ross (Thu May 12 2005 - 13:08:34 PDT)
AMBER: Trouble with example tutorial Maciej (Wed May 11 2005 - 04:08:02 PDT)
- Re: AMBER: Trouble with example tutorial David A. Case (Thu May 12 2005 - 10:04:51 PDT)
AMBER: Parameter for alpha-lactose Sagarika Dev (Wed May 11 2005 - 07:48:21 PDT)
- Re: AMBER: Parameter for alpha-lactose David A. Case (Thu May 12 2005 - 08:29:08 PDT)
AMBER: Asking how to creat alanine "dipeptide" in amber8 Li Su (Wed May 11 2005 - 08:37:07 PDT)
- Re: AMBER: Asking how to creat alanine "dipeptide" in amber8 Thomas E. Cheatham, III (Wed May 11 2005 - 08:38:54 PDT)
- Re: AMBER: Asking how to creat alanine "dipeptide" in amber8 FyD (Wed May 11 2005 - 09:06:27 PDT)
- RE: AMBER: Asking how to creat alanine "dipeptide" in amber8 Ross Walker (Wed May 11 2005 - 10:13:30 PDT)
Fwd: Re: AMBER: AMBER Test Anthony Cruz (Wed May 11 2005 - 08:49:38 PDT)
- Re: Fwd: Re: AMBER: AMBER Test David A. Case (Thu May 12 2005 - 08:33:15 PDT)
AMBER: SANDER BOMB: volume of ucell too big Stern, Julie (Wed May 11 2005 - 09:07:38 PDT)
- Re: AMBER: SANDER BOMB: volume of ucell too big Michael Crowley (Thu May 12 2005 - 10:10:20 PDT)
- RE: AMBER: SANDER BOMB: volume of ucell too big Stern, Julie (Thu May 12 2005 - 12:34:55 PDT)
  - Re: AMBER: SANDER BOMB: volume of ucell too big David A. Case (Thu May 12 2005 - 13:27:50 PDT)
    - Re: AMBER: SANDER BOMB: volume of ucell too big Robert Duke (Thu May 12 2005 - 13:44:11 PDT)
AMBER: maximum number of processors MURAT CETINKAYA (Wed May 11 2005 - 20:53:44 PDT)
- Re: AMBER: maximum number of processors Asim Okur (Thu May 12 2005 - 08:41:25 PDT)
- Re: AMBER: maximum number of processors Michael Crowley (Thu May 12 2005 - 10:00:09 PDT)
- Re: AMBER: maximum number of processors Abd Ghani Abd Aziz (Fri May 13 2005 - 23:42:49 PDT)
  - Re: AMBER: maximum number of processors C J Kenneth Tan -- OptimaNumerics (Sat May 14 2005 - 07:57:22 PDT)
AMBER: RESP charge fitting for N-methylguanine cation Grzegorz Jezierski (Thu May 12 2005 - 09:50:17 PDT)
- Re: AMBER: RESP charge fitting for N-methylguanine cation Kara Di Giorgio (Thu May 12 2005 - 19:40:17 PDT)
- Re: AMBER: RESP charge fitting for N-methylguanine cation FyD (Fri May 13 2005 - 08:33:05 PDT)
AMBER: Tutorial #1 ptraj/sander problem Daniela Kohen (Thu May 12 2005 - 15:03:07 PDT)
- RE: AMBER: Tutorial #1 ptraj/sander problem Ross Walker (Thu May 12 2005 - 15:33:44 PDT)
AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang (Thu May 12 2005 - 18:44:04 PDT)
- Re: AMBER: the restraint MD fail with amber8,but success with amber7 Carlos Simmerling (Fri May 13 2005 - 03:50:10 PDT)
  - Re: AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang (Fri May 13 2005 - 04:19:20 PDT)
    - Re: AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang (Fri May 13 2005 - 04:21:28 PDT)
AMBER: amber8 test error Cordova, Luis E. (Thu May 12 2005 - 20:26:00 PDT)
- Re: AMBER: amber8 test error David A. Case (Fri May 13 2005 - 10:11:27 PDT)
AMBER: creating residues - charge assign problems Hayden Eastwood (Fri May 13 2005 - 04:06:06 PDT)
- Re: AMBER: creating residues - charge assign problems FyD (Fri May 13 2005 - 08:25:48 PDT)
- Re: AMBER: creating residues - charge assign problems David A. Case (Fri May 13 2005 - 09:43:41 PDT)
AMBER: platinum atom in Xleap Chen Chengwen (Fri May 13 2005 - 19:11:12 PDT)
AMBER: How to create a parallel job for amber 8? Ò×ºç (Sat May 14 2005 - 04:20:15 PDT)
- Re: AMBER: How to create a parallel job for amber 8? Shulin Zhuang (Sat May 14 2005 - 06:45:54 PDT)
AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? caoch.cherry.bio.titech.ac.jp (Sat May 14 2005 - 10:17:17 PDT)
- Re: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? Carlos Simmerling (Sat May 14 2005 - 10:52:56 PDT)
- RE: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? ross.rosswalker.co.uk (Sat May 14 2005 - 12:43:46 PDT)
  - AMBER: amber 8 REM possible test problem Sergio E. Wong (Tue May 17 2005 - 14:51:04 PDT)
AMBER: Calculating of radius of gyration in Carnal Hwankyu Lee (Sat May 14 2005 - 11:36:37 PDT)
Re: AMBER: Calculating of radius of gyration in Carnal Bill Ross (Sat May 14 2005 - 15:26:43 PDT)
AMBER: how to reduce box size and delete excess solvent hj zou (Sun May 15 2005 - 04:51:32 PDT)
AMBER: How to set constraint Li Su (Sun May 15 2005 - 11:58:51 PDT)
- Re: AMBER: How to set constraint David A. Case (Mon May 16 2005 - 08:42:27 PDT)
Re: AMBER: how to reduce box size and delete excess solvent Bill Ross (Sun May 15 2005 - 12:50:01 PDT)
AMBER: strange mm_pbsa.pl bug Nelson Fonseca (Mon May 16 2005 - 08:39:21 PDT)
AMBER: How to set up dihedral constraints in amber Li Su (Mon May 16 2005 - 08:39:50 PDT)
AMBER: generating over 16 bps of DNA in nucgen Hwankyu Lee (Mon May 16 2005 - 08:33:04 PDT)
- Re: AMBER: generating over 16 bps of DNA in nucgen Garhan Attebury (Tue May 17 2005 - 08:27:13 PDT)
  - Re: AMBER: generating over 16 bps of DNA in nucgen aanzellotti.mail2.vcu.edu (Tue May 17 2005 - 08:57:45 PDT)
AMBER: output of force field info Stern, Julie (Mon May 16 2005 - 12:24:37 PDT)
- Re: AMBER: output of force field info David A. Case (Mon May 16 2005 - 17:16:55 PDT)
- Re: AMBER: output of force field info Thomas E. Cheatham, III (Mon May 16 2005 - 18:21:51 PDT)
  - AMBER: ATOM TYPE Ilyas Yildirim (Mon May 16 2005 - 19:10:48 PDT)
AMBER: nmode in mmpbsa Joseph Fernandez (Mon May 16 2005 - 16:36:28 PDT)
- AMBER: *** Proper torsion parameters missing *** Ilyas Yildirim (Mon May 16 2005 - 17:19:04 PDT)
  - AMBER: gaff: ca-ca-c -o torsion parameter Oliver Hucke (Tue May 17 2005 - 13:54:24 PDT)
    - Re: AMBER: gaff: ca-ca-c -o torsion parameter David A. Case (Tue May 17 2005 - 23:38:33 PDT)
- Re: AMBER: nmode in mmpbsa Holger Gohlke (Mon May 16 2005 - 23:44:17 PDT)
AMBER: MMPBSA calculations on Highly charged systems Vitor Manuel Sousa F?x (Tue May 17 2005 - 04:01:21 PDT)
- Re: AMBER: MMPBSA calculations on Highly charged systems Nelson Fonseca (Tue May 17 2005 - 05:36:16 PDT)
AMBER: Message in .out file Atilio Anzellotti (Tue May 17 2005 - 05:31:36 PDT)
- Re: AMBER: Message in .out file David A. Case (Tue May 17 2005 - 23:38:40 PDT)
AMBER: GAFF angle parameters Monica Civera (Tue May 17 2005 - 09:11:46 PDT)
- RE: AMBER: GAFF angle parameters Junmei Wang (Tue May 17 2005 - 15:08:47 PDT)
AMBER: molsurf error mingche Pan (Tue May 17 2005 - 09:52:57 PDT)
AMBER: compiling pmemd on dual xeon Tiziano Tuccinardi (Tue May 17 2005 - 10:28:31 PDT)
- Re: AMBER: compiling pmemd on dual xeon Robert Duke (Tue May 17 2005 - 10:49:48 PDT)
  - Re: AMBER: compiling pmemd on dual xeon Tiziano Tuccinardi (Tue May 17 2005 - 11:05:49 PDT)
AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Rajeev Ranjan Singh (Tue May 17 2005 - 13:15:33 PDT)
AMBER: RE: Tutorial#1 ptraj/sander problem Ross Walker (Tue May 17 2005 - 15:56:59 PDT)
AMBER: MD on surface Yanze Zhang (Tue May 17 2005 - 16:58:29 PDT)
AMBER: error with ptraj Xiaowei (David) Li (Tue May 17 2005 - 21:27:33 PDT)
- Re: AMBER: error with ptraj David A. Case (Tue May 17 2005 - 23:38:22 PDT)
AMBER: loading pdb cbala.igib.res.in (Tue May 17 2005 - 22:56:13 PDT)
- Re: AMBER: loading pdb David A. Case (Tue May 17 2005 - 23:38:27 PDT)
- Re: AMBER: loading pdb Rajeev Ranjan Singh (Wed May 18 2005 - 07:01:34 PDT)
- Re: AMBER: loading pdb Ilyas Yildirim (Wed May 18 2005 - 13:21:24 PDT)
AMBER: Using AMBER for Carbon nanotubes Zhang Yingyan (Wed May 18 2005 - 01:21:42 PDT)
- RE: AMBER: Using AMBER for Carbon nanotubes Ross Walker (Wed May 18 2005 - 10:12:29 PDT)
AMBER: error during MD run cbala.igib.res.in (Wed May 18 2005 - 11:39:25 PDT)
- Re: AMBER: error during MD run Thomas E. Cheatham, III (Wed May 18 2005 - 11:10:36 PDT)
- Re: AMBER: error during MD run Rajeev Ranjan Singh (Wed May 18 2005 - 11:16:12 PDT)
AMBER: frcmod info for Nickel Kara Di Giorgio (Wed May 18 2005 - 12:04:44 PDT)
AMBER: parameter for sulfur in thio-glucoside residue Vijay Manickam Achari (Wed May 18 2005 - 18:58:57 PDT)
- Re: AMBER: parameter for sulfur in thio-glucoside residue Ilyas Yildirim (Wed May 18 2005 - 19:11:34 PDT)
AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim (Wed May 18 2005 - 19:16:35 PDT)
- Re: AMBER: Can we load prmtop and inpcrd files into xleap? Kara Di Giorgio (Wed May 18 2005 - 19:45:43 PDT)
  - Re: AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim (Wed May 18 2005 - 21:00:07 PDT)
    - Re: AMBER: Can we load prmtop and inpcrd files into xleap? Kara Di Giorgio (Wed May 18 2005 - 21:10:36 PDT)
    - Re: AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim (Wed May 18 2005 - 21:47:49 PDT)
- Re: AMBER: Can we load prmtop and inpcrd files into xleap? Bill Ross (Wed May 18 2005 - 21:49:04 PDT)
AMBER: Amber 8 and LAM compilation problem Glen Otero (Wed May 18 2005 - 22:52:00 PDT)
- Re: AMBER: Amber 8 and LAM compilation problem Robert Duke (Thu May 19 2005 - 05:05:48 PDT)
AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Vijay Manickam Achari (Wed May 18 2005 - 23:55:21 PDT)
- RE: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Ross Walker (Thu May 19 2005 - 00:16:41 PDT)
- Re: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Ilyas Yildirim (Thu May 19 2005 - 00:37:22 PDT)
- Re: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Cenk Andac (Thu May 19 2005 - 10:03:43 PDT)
  - AMBER: Re: antechamber not working .. for thio residue.. Vijay Manickam Achari (Fri May 20 2005 - 02:32:19 PDT)
    - Re: AMBER: Re: antechamber not working .. for thio residue.. Shulin Zhuang (Fri May 20 2005 - 03:22:39 PDT)
AMBER: GB - igb=1 versus dielc=? milion.c-box.cz (Thu May 19 2005 - 09:53:00 PDT)
- Re: AMBER: GB - igb=1 versus dielc=? David A. Case (Thu May 19 2005 - 09:09:47 PDT)
AMBER: write format of restart crd in sander/pmemd Peter Varnai (Thu May 19 2005 - 05:12:22 PDT)
AMBER: Using amber4 generated prep files in amber8? Simon Whitehead (Thu May 19 2005 - 05:51:00 PDT)
- Re: AMBER: Using amber4 generated prep files in amber8? David A. Case (Thu May 19 2005 - 08:31:54 PDT)
AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 18:19:04 PDT)
- Re: AMBER: read pdb back to xleap after solvation of chloroform David A. Case (Thu May 19 2005 - 18:38:49 PDT)
  - Re: AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 18:59:47 PDT)
- RE: AMBER: read pdb back to xleap after solvation of chloroform Ross Walker (Thu May 19 2005 - 18:41:31 PDT)
  - RE: AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 19:05:27 PDT)
- RE: AMBER: read pdb back to xleap after solvation of chloroform Bill Ross (Thu May 19 2005 - 19:16:22 PDT)
  - RE: AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 19:55:23 PDT)
- RE: AMBER: read pdb back to xleap after solvation of chloroform Bill Ross (Thu May 19 2005 - 20:56:58 PDT)
- Re: AMBER: read pdb back to xleap after solvation of chloroform Furse, Kristina Elisabet (Fri May 20 2005 - 14:20:55 PDT)
AMBER: MM_PBSA for NMR restrained structures Cenk Andac (Fri May 20 2005 - 01:36:10 PDT)
AMBER: Representation of cations in MD Thomas Steinbrecher (Fri May 20 2005 - 02:30:24 PDT)
- Re: AMBER: Representation of cations in MD David A. Case (Fri May 20 2005 - 08:16:15 PDT)
AMBER: leap problem: savepdb Hannes Barsch (Fri May 20 2005 - 02:30:29 PDT)
- Re: AMBER: leap problem: savepdb David A. Case (Fri May 20 2005 - 08:21:13 PDT)
AMBER: how to creat leaprc.gaff Vijay Manickam Achari (Fri May 20 2005 - 02:36:25 PDT)
- Re: AMBER: how to creat leaprc.gaff Ilyas Yildirim (Fri May 20 2005 - 02:48:14 PDT)
AMBER: Error in minimization Priti Hansia (Fri May 20 2005 - 03:58:36 PDT)
- Re: AMBER: Error in minimization Carlos Simmerling (Fri May 20 2005 - 05:57:37 PDT)
AMBER: Steve Seibold (Fri May 20 2005 - 10:45:24 PDT)
- Re: AMBER: luckyang.gmail.com (Fri May 20 2005 - 11:28:17 PDT)
- Re: AMBER: JunJun Liu (Fri May 20 2005 - 19:41:24 PDT)
AMBER: crashing xleap Kenley Barrett (Fri May 20 2005 - 11:48:13 PDT)
- Re: AMBER: crashing xleap Scott Brozell (Fri May 20 2005 - 13:03:40 PDT)
  - Re: AMBER: crashing xleap Kenley Barrett (Fri May 20 2005 - 13:57:00 PDT)
    - Re: AMBER: crashing xleap Ilyas Yildirim (Fri May 20 2005 - 14:47:09 PDT)
- Re: AMBER: crashing xleap Furse, Kristina Elisabet (Fri May 20 2005 - 15:28:05 PDT)
  - Re: AMBER: crashing xleap; bugfix.44 Scott Brozell (Mon May 23 2005 - 10:22:51 PDT)
AMBER: 1-4 scaling factors Stern, Julie (Fri May 20 2005 - 12:13:22 PDT)
- Re: AMBER: 1-4 scaling factors Thomas E. Cheatham, III (Fri May 20 2005 - 12:43:34 PDT)
Re: AMBER: crashing xleap Bill Ross (Fri May 20 2005 - 12:55:15 PDT)
AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Sun May 22 2005 - 12:44:55 PDT)
- Re: AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Mon May 23 2005 - 00:14:54 PDT)
- Re: AMBER: Unexpected stop of Sander run Carlos Simmerling (Mon May 23 2005 - 04:15:34 PDT)
  - Re: AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Mon May 23 2005 - 06:43:51 PDT)
    - Re: AMBER: Unexpected stop of Sander run Carlos Simmerling (Mon May 23 2005 - 06:57:00 PDT)
    - Re: AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Mon May 23 2005 - 07:38:58 PDT)
- Re: AMBER: Unexpected stop of Sander run David A. Case (Mon May 23 2005 - 08:00:46 PDT)
AMBER: Copyright for PBSA Cenk Andac (Sat May 21 2005 - 01:32:00 PDT)
- Re: AMBER: Copyright for PBSA David A. Case (Sat May 21 2005 - 20:37:45 PDT)
AMBER: Citing the PBSA module of AMBER8 Cenk Andac (Fri May 20 2005 - 14:27:03 PDT)
AMBER: rotating and repositioning molecules in xleap Hwankyu Lee (Fri May 20 2005 - 23:09:45 PDT)
- Re: AMBER: rotating and repositioning molecules in xleap Angelo Pugliese (Sun May 22 2005 - 02:37:44 PDT)
  - Re: AMBER: rotating and repositioning molecules in xleap Hwankyu Lee (Sun May 22 2005 - 06:03:40 PDT)
- Re: AMBER: rotating and repositioning molecules in xleap Bill Ross (Sun May 22 2005 - 08:36:16 PDT)
AMBER: modeller Zhang Bing (Fri May 20 2005 - 21:53:13 PDT)
Re: AMBER: Unexpected stop of Sander run Bill Ross (Sun May 22 2005 - 13:18:16 PDT)
- Re: AMBER: Unexpected stop of Sander run Carlos Simmerling (Sun May 22 2005 - 13:22:11 PDT)
AMBER: Error in sander: stack trace terminated abnormally. Hwankyu Lee (Sun May 22 2005 - 14:05:31 PDT)
- RE: AMBER: Error in sander: stack trace terminated abnormally. Ross Walker (Sun May 22 2005 - 14:53:36 PDT)
AMBER: antechamber not working .. for thio residue.. Vijay Manickam Achari (Sun May 22 2005 - 19:15:20 PDT)
- Re: AMBER: antechamber not working .. for thio residue.. Shulin Zhuang (Sun May 22 2005 - 19:31:27 PDT)
AMBER: Setting Amber force field parameters Chen Chengwen (Mon May 23 2005 - 00:55:38 PDT)
AMBER: using antechamber ... to get prepin file Vijay Manickam Achari (Mon May 23 2005 - 01:59:16 PDT)
- RE: AMBER: using antechamber ... to get prepin file Vineet Pande (Mon May 23 2005 - 05:02:26 PDT)
AMBER: Connecting two molecules Hwankyu Lee (Mon May 23 2005 - 08:13:00 PDT)
- Re: AMBER: Connecting two molecules David A. Case (Mon May 23 2005 - 08:23:51 PDT)
  - Re: AMBER: Connecting two molecules Hwankyu Lee (Mon May 23 2005 - 09:51:20 PDT)
    - AMBER: hbond detailed analysis over time? pascal.baillod.epfl.ch (Mon May 23 2005 - 11:04:10 PDT)
AMBER: how to generate frcmod file for using prepin file.. Vijay Manickam Achari (Mon May 23 2005 - 19:52:18 PDT)
- RE: AMBER: how to generate frcmod file for using prepin file.. chaiann ng (Mon May 23 2005 - 20:03:55 PDT)
AMBER: my frcmod file created using parmchk Vijay Manickam Achari (Mon May 23 2005 - 20:44:21 PDT)
- Re: AMBER: my frcmod file created using parmchk Ilyas Yildirim (Mon May 23 2005 - 21:03:42 PDT)
AMBER: my prepin file in lowe-case Vijay Manickam Achari (Tue May 24 2005 - 00:51:55 PDT)
AMBER: Which forcefield? Simon Whitehead (Tue May 24 2005 - 01:13:01 PDT)
- Re: AMBER: Which forcefield? David A. Case (Tue May 24 2005 - 22:32:09 PDT)
AMBER: conformational sampling of a peptide Hannes Barsch (Tue May 24 2005 - 01:58:04 PDT)
- Re: AMBER: conformational sampling of a peptide Joseph Nachman (Tue May 24 2005 - 08:26:52 PDT)
AMBER: amber code Juan Fernandez Carmona (Tue May 24 2005 - 03:08:00 PDT)
- Re: AMBER: amber code Andreas Svrcek-Seiler (Tue May 24 2005 - 07:18:11 PDT)
Re: AMBER: conformational sampling of a peptide Carlos Simmerling (Tue May 24 2005 - 06:11:53 PDT)
AMBER: Fw: Installing PMEMD on IBM machine (CPU power4) running SUSE_9.1 Robert Duke (Tue May 24 2005 - 07:42:15 PDT)
AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_' René Ranzinger (Tue May 24 2005 - 08:04:42 PDT)
- RE: AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_' Ross Walker (Tue May 24 2005 - 08:43:37 PDT)
AMBER: Sander Restart Problem Garhan Attebury (Tue May 24 2005 - 08:07:49 PDT)
AMBER: How to fix certain bond angles Li Su (Tue May 24 2005 - 08:27:14 PDT)
- Re: AMBER: How to fix certain bond angles Guanglei Cui (Tue May 24 2005 - 08:40:00 PDT)
AMBER: Error: vlimit exceeded for step Hwankyu Lee (Tue May 24 2005 - 10:20:10 PDT)
- Re: AMBER: Error: vlimit exceeded for step Carlos Simmerling (Tue May 24 2005 - 10:51:14 PDT)
  - Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee (Tue May 24 2005 - 11:07:41 PDT)
    - Re: AMBER: Error: vlimit exceeded for step Thomas E. Cheatham, III (Tue May 24 2005 - 11:12:58 PDT)
    - Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee (Tue May 24 2005 - 11:34:34 PDT)
    - Re: AMBER: Error: vlimit exceeded for step David Mobley (Tue May 24 2005 - 12:27:23 PDT)
Solute-solvent boundary in pbsa ..Re: AMBER: Copyright for PBSA Cenk Andac (Tue May 24 2005 - 11:48:26 PDT)
- Re: AMBER: Solute-solvent boundary in pbsa Ray Luo (Tue May 24 2005 - 01:48:10 PDT)
  - Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac (Wed May 25 2005 - 09:21:52 PDT)
    - Re: AMBER: Solute-solvent boundary in pbsa Ray Luo (Tue May 24 2005 - 22:54:50 PDT)
  - Re:Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac (Thu May 26 2005 - 13:58:55 PDT)
    - Re: AMBER: Solute-solvent boundary in pbsa Ray Luo (Wed May 25 2005 - 18:40:39 PDT)
AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Li Su (Tue May 24 2005 - 12:14:09 PDT)
- Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Petr Kulhanek (Wed May 25 2005 - 04:56:34 PDT)
  - Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Guanglei Cui (Wed May 25 2005 - 06:55:23 PDT)
    - Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Petr Kulhanek (Thu May 26 2005 - 03:44:37 PDT)
AMBER: charges difference of atom in xleap and prmtop chaiann ng (Tue May 24 2005 - 21:02:33 PDT)
- Re: AMBER: charges difference of atom in xleap and prmtop David A. Case (Tue May 24 2005 - 22:27:51 PDT)
AMBER: PARMSCAN program Philippe ARNAUD (Wed May 25 2005 - 00:28:31 PDT)
AMBER: average structure after MD kuljeets.igib.res.in (Wed May 25 2005 - 02:14:19 PDT)
- Re: AMBER: average structure after MD kuljeets.igib.res.in (Wed May 25 2005 - 22:42:32 PDT)
AMBER: quadrupole in resp riccardo nifosi (Wed May 25 2005 - 03:44:20 PDT)
AMBER: error in chirality.c? Kenley Barrett (Wed May 25 2005 - 07:27:07 PDT)
- Re: AMBER: error in chirality.c? David A. Case (Wed May 25 2005 - 08:21:48 PDT)
Re#2:Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac (Wed May 25 2005 - 13:03:47 PDT)
- Re: Re#2:Re: AMBER: Solute-solvent boundary in pbsa Ray Luo (Tue May 24 2005 - 22:56:08 PDT)
AMBER: dissolving micelle structure in water.. amber7 Vijay Manickam Achari (Wed May 25 2005 - 20:59:22 PDT)
- Re: AMBER: dissolving micelle structure in water.. amber7 David A. Case (Thu May 26 2005 - 09:30:17 PDT)
- Re: AMBER: dissolving micelle structure in water.. amber7 Bill Ross (Thu May 26 2005 - 09:50:23 PDT)
- Re: AMBER: dissolving micelle structure in water.. amber7 Vijay Manickam Achari (Thu May 26 2005 - 18:19:57 PDT)
AMBER: distance restraints between two centers of mass JAVIER PEREZ (Thu May 26 2005 - 01:37:30 PDT)
- Re: AMBER: distance restraints between two centers of mass Fabien Cailliez (Thu May 26 2005 - 02:01:08 PDT)
AMBER: Is the MD simulation normal Shulin Zhuang (Thu May 26 2005 - 08:30:48 PDT)
- RE: AMBER: Is the MD simulation normal Yong Duan (Thu May 26 2005 - 10:05:14 PDT)
- Re: AMBER: Is the MD simulation normal Thomas E. Cheatham, III (Thu May 26 2005 - 10:41:03 PDT)
  - Re: AMBER: Is the MD simulation normal Shulin Zhuang (Thu May 26 2005 - 21:23:37 PDT)
    - RE: AMBER: Is the MD simulation normal Yong Duan (Thu May 26 2005 - 23:17:00 PDT)
    - Re: AMBER: Is the MD simulation normal Shulin Zhuang (Fri May 27 2005 - 00:38:05 PDT)
    - RE: AMBER: Is the MD simulation normal Yong Duan (Fri May 27 2005 - 09:31:27 PDT)
- Re: AMBER: Is the MD simulation normal Bill Ross (Fri May 27 2005 - 11:14:30 PDT)
  - Re: AMBER: Is the MD simulation normal Shulin Zhuang (Sat May 28 2005 - 06:02:05 PDT)
- Re: AMBER: Is the MD simulation normal Bill Ross (Sat May 28 2005 - 10:00:42 PDT)
  - Re: AMBER: Is the MD simulation normal Shulin Zhuang (Sun May 29 2005 - 07:53:35 PDT)
    - RE: AMBER: Is the MD simulation normal Yong Duan (Sun May 29 2005 - 09:46:44 PDT)
- Re: AMBER: Is the MD simulation normal Bill Ross (Sun May 29 2005 - 08:33:13 PDT)
- RE: AMBER: Is the MD simulation normal Bill Ross (Sun May 29 2005 - 10:04:01 PDT)
  - Re: AMBER: Is the MD simulation normal Shulin Zhuang (Mon May 30 2005 - 07:39:50 PDT)
- Re: AMBER: Is the MD simulation normal Bill Ross (Mon May 30 2005 - 09:49:32 PDT)
- Re: AMBER: Is the MD simulation normal Bill Ross (Tue May 31 2005 - 20:41:42 PDT)
AMBER: setting up Parallel processing mathew k varghese (Thu May 26 2005 - 08:39:00 PDT)
- Re: AMBER: setting up Parallel processing Robert Duke (Thu May 26 2005 - 09:15:30 PDT)
- RE: AMBER: setting up Parallel processing 'Ross Walker' (Thu May 26 2005 - 11:14:18 PDT)
AMBER: hbond analysis in ptaj/carnal Jana Precechtelova (Thu May 26 2005 - 09:25:20 PDT)
- Re: AMBER: hbond analysis in ptaj/carnal Thomas E. Cheatham, III (Thu May 26 2005 - 10:05:00 PDT)
Re: AMBER: hbond analysis in ptaj/carnal Bill Ross (Thu May 26 2005 - 09:44:13 PDT)
AMBER: why is snaupe.f is empty? Cordova, Luis E. (Thu May 26 2005 - 10:06:24 PDT)
- RE: AMBER: why is snaupe.f is empty? 'Ross Walker' (Thu May 26 2005 - 11:14:34 PDT)
AMBER: ptraj - hbond detailed analysis over time? pascal.baillod.epfl.ch (Thu May 26 2005 - 10:38:38 PDT)
AMBER: Mol2 to prepin file conversion Andrew Box (Thu May 26 2005 - 17:08:22 PDT)
- Re: AMBER: Mol2 to prepin file conversion David A. Case (Thu May 26 2005 - 17:44:36 PDT)
AMBER: question about loadiing pdb file of a molecule complex gtg549i.mail.gatech.edu (Fri May 27 2005 - 14:39:28 PDT)
- Re: AMBER: question about loadiing pdb file of a molecule complex Chutintorn Punwong (Fri May 27 2005 - 15:07:52 PDT)
- Re: AMBER: question about loadiing pdb file of a molecule complex David A. Case (Sat May 28 2005 - 22:29:53 PDT)
  - AMBER: Reference (?) for normal-mode analysis in nmode Cenk Andac (Mon May 30 2005 - 02:18:59 PDT)
    - Re: AMBER: Reference (?) for normal-mode analysis in nmode David A. Case (Tue May 31 2005 - 08:30:10 PDT)
  - Re: AMBER: question about loadiing pdb file of a molecule complex gtg549i.mail.gatech.edu (Mon May 30 2005 - 08:56:09 PDT)
    - Re: AMBER: question about loadiing pdb file of a molecule complex David A. Case (Tue May 31 2005 - 11:00:59 PDT)
    - Re: AMBER: question about loadiing pdb file of a molecule complex gtg549i.mail.gatech.edu (Tue May 31 2005 - 12:12:39 PDT)
AMBER: Workshop Tutorials Downtime this weekend. Ross Walker (Fri May 27 2005 - 14:49:05 PDT)
AMBER: Antechamber RESP failed for large organic molecule junwang (Sun May 29 2005 - 12:57:59 PDT)
- Re: AMBER: Antechamber RESP failed for large organic molecule David A. Case (Mon May 30 2005 - 09:09:27 PDT)
- RE: AMBER: Antechamber RESP failed for large organic molecule Junmei Wang (Tue May 31 2005 - 07:37:35 PDT)
  - Re: RE: AMBER: Antechamber RESP failed for large organic molecule junwang (Tue May 31 2005 - 09:58:33 PDT)
AMBER: question about initial conditions for amber Ed Pate (Sun May 29 2005 - 19:42:21 PDT)
- Re: AMBER: question about initial conditions for amber Stefano Federico Pieraccini (Mon May 30 2005 - 04:44:54 PDT)
- Re: AMBER: question about initial conditions for amber Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Mon May 30 2005 - 04:40:59 PDT)
AMBER: density profiles in ptraj or carnal Hwankyu Lee (Sun May 29 2005 - 20:27:37 PDT)
AMBER: pairwise energy decomposition using MM-PBSA Xin Hu (Sun May 29 2005 - 20:38:30 PDT)
AMBER: Force field modification problem yuann (Mon May 30 2005 - 04:16:27 PDT)
- Re: AMBER: Force field modification problem David A. Case (Mon May 30 2005 - 09:21:00 PDT)
  - Re[2]: AMBER: Force field modification problem sychen (Mon May 30 2005 - 17:05:45 PDT)
    - Re: AMBER: Force field modification problem David A. Case (Mon May 30 2005 - 22:17:06 PDT)
AMBER: Bond angle restraints setting files Li Su (Mon May 30 2005 - 09:05:15 PDT)
Re: AMBER: density profiles in ptraj or carnal Bill Ross (Mon May 30 2005 - 10:00:08 PDT)
- Re: AMBER: density profiles in ptraj or carnal Hwankyu Lee (Mon May 30 2005 - 15:58:54 PDT)
  - Re: AMBER: density profiles in ptraj or carnal Hwankyu Lee (Mon May 30 2005 - 21:13:26 PDT)
- Re: AMBER: density profiles in ptraj or carnal Bill Ross (Tue May 31 2005 - 09:13:28 PDT)
AMBER: density problem cristian obiol (Tue May 31 2005 - 02:17:46 PDT)
- RE: AMBER: density problem Ross Walker (Tue May 31 2005 - 08:33:39 PDT)
AMBER: stack terminated abnormally drugdesign (Tue May 31 2005 - 03:20:33 PDT)
- RE: AMBER: stack terminated abnormally Ross Walker (Tue May 31 2005 - 08:35:15 PDT)
AMBER: if setting ntf=4, will it cause someproblem? Li Su (Tue May 31 2005 - 07:55:03 PDT)
- Re: AMBER: if setting ntf=4, will it cause someproblem? Carlos Simmerling (Tue May 31 2005 - 08:12:30 PDT)
  - Re: AMBER: if setting ntf=4, will it cause someproblem? Li Su (Tue May 31 2005 - 14:07:25 PDT)
AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Tue May 31 2005 - 08:23:51 PDT)
- Re: AMBER: Error on restrained MD equilibration (AMBER 7) David A. Case (Tue May 31 2005 - 08:45:01 PDT)
- Re: AMBER: Error on restrained MD equilibration (AMBER 7) Viktor Hornak (Tue May 31 2005 - 08:52:48 PDT)
- Re: AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Tue May 31 2005 - 09:21:55 PDT)
  - RE: AMBER: Error on restrained MD equilibration (AMBER 7) Ross Walker (Tue May 31 2005 - 09:45:19 PDT)
  - AMBER: runtime error in sander? Dave S Walker (Tue May 31 2005 - 10:07:13 PDT)
    - RE: AMBER: runtime error in sander? Ross Walker (Tue May 31 2005 - 10:34:51 PDT)
  - Re: AMBER: Error on restrained MD equilibration (AMBER 7) Guanglei Cui (Tue May 31 2005 - 12:02:46 PDT)
AMBER: DNA base-flipping: TI vs PMF Lauren O'Neil (Tue May 31 2005 - 08:40:45 PDT)
AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Grzegorz Jezierski (Tue May 31 2005 - 09:04:20 PDT)
- RE: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Ross Walker (Tue May 31 2005 - 09:09:20 PDT)
- Re: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Marcin Krol (Tue May 31 2005 - 09:17:30 PDT)
AMBER: MM-PBSA calculation masi.nmr.mpibpc.mpg.de (Tue May 31 2005 - 09:37:40 PDT)
- AMBER: Loading pdb-residue (re)numbering in leap gtg549i.mail.gatech.edu (Tue May 31 2005 - 10:48:13 PDT)
AMBER: STOP 0 masi.nmr.mpibpc.mpg.de (Tue May 31 2005 - 09:40:25 PDT)
- RE: AMBER: STOP 0 Ross Walker (Tue May 31 2005 - 09:47:20 PDT)
AMBER:Sander errors: Unit 6 Error on OPEN: mdout Douali, Latifa (Tue May 31 2005 - 10:34:41 PDT)
- RE: AMBER:Sander errors: Unit 6 Error on OPEN: mdout Ross Walker (Tue May 31 2005 - 10:45:53 PDT)
- RE: AMBER:Sander errors: Unit 6 Error on OPEN: mdout Bill Ross (Tue May 31 2005 - 11:42:50 PDT)
Re: AMBER: STOP 0 Bill Ross (Tue May 31 2005 - 10:43:32 PDT)
AMBER: meaningful tax for sander question Cordova, Luis E. (Tue May 31 2005 - 12:19:30 PDT)
- RE: AMBER: meaningful tax for sander question Ross Walker (Tue May 31 2005 - 12:55:14 PDT)
- Re: AMBER: meaningful tax for sander question David A. Case (Tue May 31 2005 - 12:59:20 PDT)
- RE: AMBER: meaningful tax for sander question Cordova, Luis E. (Tue May 31 2005 - 13:03:59 PDT)
- RE: AMBER: meaningful tax for sander question Ross Walker (Tue May 31 2005 - 13:12:10 PDT)
AMBER: double counting of potentials Stern, Julie (Tue May 31 2005 - 16:04:43 PDT)
- RE: AMBER: double counting of potentials Ross Walker (Tue May 31 2005 - 16:21:43 PDT)
AMBER: Working with a nickel-organometallic compound Kara Di Giorgio (Tue May 31 2005 - 16:36:30 PDT)
AMBER: External Field in AMBER? junwang (Tue May 31 2005 - 19:19:38 PDT)

Amber Archive May 2005 By Thread