AMBER Archive (2009) - Nov 2009 By Date

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Starting: Sun Nov 01 2009 - 11:59:34 CST
Ending: Mon Nov 30 2009 - 23:59:05 CST

[AMBER] retinal lib file, params? Mark M Huntress (Sun Nov 01 2009 - 11:59:34 CST)
[AMBER] Re: RESP with -a and witout -a flag Jio M (Sun Nov 01 2009 - 23:58:58 CST)
[AMBER] Is it taking too much time nicholus bhattacharjee (Mon Nov 02 2009 - 00:08:46 CST)
Re: [AMBER] Is it taking too much time manoj singh (Mon Nov 02 2009 - 01:31:07 CST)
Re: [AMBER] retinal lib file, params? Simon Becker (Mon Nov 02 2009 - 02:34:14 CST)
Re: [AMBER] Is it taking too much time nicholus bhattacharjee (Mon Nov 02 2009 - 02:37:28 CST)
[AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Mon Nov 02 2009 - 03:17:19 CST)
Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Jason Swails (Mon Nov 02 2009 - 06:15:19 CST)
Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Mon Nov 02 2009 - 07:11:15 CST)
Re: [AMBER] Is it taking too much time manoj singh (Mon Nov 02 2009 - 07:50:21 CST)
[AMBER] amber 10 test failures... peker milas (Mon Nov 02 2009 - 08:18:29 CST)
Re: [AMBER] Is it taking too much time Nicolas SAPAY (Mon Nov 02 2009 - 08:19:17 CST)
Re: [AMBER] Is it taking too much time nicholus bhattacharjee (Mon Nov 02 2009 - 08:40:25 CST)
Re: [AMBER] Is it taking too much time Nicolas SAPAY (Mon Nov 02 2009 - 09:00:58 CST)
Re: [AMBER] Gaussian log file error Ben Roberts (Mon Nov 02 2009 - 09:16:23 CST)
Re: [AMBER] Gaussian log file error Junmei Wang (Mon Nov 02 2009 - 09:58:10 CST)
Re: [AMBER] Re: RESP with -a and witout -a flag Junmei Wang (Mon Nov 02 2009 - 10:48:48 CST)
Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Jason Swails (Mon Nov 02 2009 - 11:04:14 CST)
[AMBER] 60 giga output file .mdcrd file Silvia Carlotto (Mon Nov 02 2009 - 11:41:32 CST)
Re: [AMBER] 60 giga output file .mdcrd file Peter Schmidtke (Mon Nov 02 2009 - 12:40:48 CST)
[AMBER] Is it possible to simulate transmembrane protein with GB model ? cgji (Mon Nov 02 2009 - 14:52:44 CST)
RE: [AMBER] 60 giga output file .mdcrd file Ross Walker (Mon Nov 02 2009 - 17:36:48 CST)
RE: [AMBER] MPI process terminated unexpectedly after cluster upgrade Ross Walker (Mon Nov 02 2009 - 17:36:48 CST)
RE: [AMBER] amber 10 test failures... Ross Walker (Mon Nov 02 2009 - 17:36:48 CST)
[AMBER] RE: question Ross Walker (Mon Nov 02 2009 - 17:36:48 CST)
RE: [AMBER] Is it taking too much time Ross Walker (Mon Nov 02 2009 - 17:36:48 CST)
Re: [AMBER] amber 10 test failures... Mark Williamson (Mon Nov 02 2009 - 18:11:40 CST)
Re: [AMBER] amber 10 test failures... Jason Swails (Mon Nov 02 2009 - 18:19:43 CST)
[AMBER] sander.APBS install problem Rilei Yu (Mon Nov 02 2009 - 19:58:30 CST)
Re: [AMBER] sander.APBS install problem Robert Konecny (Mon Nov 02 2009 - 22:52:09 CST)
Re: [AMBER] Is it taking too much time nicholus bhattacharjee (Mon Nov 02 2009 - 23:14:26 CST)
Re: [AMBER] Is it taking too much time nicholus bhattacharjee (Mon Nov 02 2009 - 23:35:04 CST)
Re: [AMBER] Some queries about pH simulation nicholus bhattacharjee (Tue Nov 03 2009 - 01:34:02 CST)
Re: [AMBER] Is it taking too much time Nicolas Sapay (Tue Nov 03 2009 - 02:57:55 CST)
Re: [AMBER] 60 giga output file .mdcrd file Silvia Carlotto (Tue Nov 03 2009 - 04:24:03 CST)
Re: [AMBER] 60 giga output file .mdcrd file Fernando Martín García (Tue Nov 03 2009 - 04:35:41 CST)
Re: [AMBER] Some queries about pH simulation case (Tue Nov 03 2009 - 05:30:07 CST)
Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Tue Nov 03 2009 - 07:20:17 CST)
Re: [AMBER] 60 giga output file .mdcrd file Jason Swails (Tue Nov 03 2009 - 07:49:01 CST)
Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Tue Nov 03 2009 - 08:06:11 CST)
Re: [AMBER] amber 10 test failures... peker milas (Tue Nov 03 2009 - 08:11:01 CST)
Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Jason Swails (Tue Nov 03 2009 - 08:11:48 CST)
RE: [AMBER] 60 giga output file .mdcrd file Richard Owczarzy (Tue Nov 03 2009 - 09:14:44 CST)
[AMBER] Phosphorylated Threonine Beale, John (Tue Nov 03 2009 - 10:31:09 CST)
Re: [AMBER] 60 giga output file .mdcrd file Silvia Carlotto (Tue Nov 03 2009 - 10:42:43 CST)
Re: [AMBER] Phosphorylated Threonine FyD (Tue Nov 03 2009 - 13:41:49 CST)
[AMBER] AMBER: segmentation fault when running parmchk Alexander Boncheff (Tue Nov 03 2009 - 13:41:55 CST)
[AMBER] error in reading namelist cntrl Giuseppe De Marco (Tue Nov 03 2009 - 13:44:01 CST)
[AMBER] Re: question Marek Maly (Tue Nov 03 2009 - 14:22:16 CST)
Re: [AMBER] AMBER: segmentation fault when running parmchk Jason Swails (Tue Nov 03 2009 - 14:22:10 CST)
Re: [AMBER] AMBER: segmentation fault when running parmchk Alexander Boncheff (Tue Nov 03 2009 - 16:29:00 CST)
RE: [AMBER] error in reading namelist cntrl Ross Walker (Tue Nov 03 2009 - 16:57:58 CST)
RE: [AMBER] 60 giga output file .mdcrd file Ross Walker (Tue Nov 03 2009 - 17:10:17 CST)
RE: [AMBER] MPI process terminated unexpectedly after cluster upgrade Ross Walker (Tue Nov 03 2009 - 17:13:45 CST)
Re: [AMBER] AMBER: segmentation fault when running parmchk Bill Ross (Tue Nov 03 2009 - 17:15:00 CST)
[AMBER] Antechamber and Parmchk problems cyk5056 (Tue Nov 03 2009 - 20:22:38 CST)
[AMBER] ambr parameter file creation and usage Donald Keidel (Tue Nov 03 2009 - 22:39:38 CST)
[AMBER] amber parameter file creation and usage Donald Keidel (Tue Nov 03 2009 - 22:47:36 CST)
Re: [AMBER] amber parameter file creation and usage Jason Swails (Tue Nov 03 2009 - 23:29:30 CST)
[AMBER] errors on leap for a RNA+Adenine pdb structure zgong.hust (Wed Nov 04 2009 - 00:18:41 CST)
[AMBER] Re: RESP with -a and witout -a flag Jio M (Wed Nov 04 2009 - 00:47:55 CST)
Re: [AMBER] errors on leap for a RNA+Adenine pdb structure case (Wed Nov 04 2009 - 06:17:53 CST)
Re: [AMBER] 60 giga output file .mdcrd file case (Wed Nov 04 2009 - 06:17:47 CST)
Re: Re: [AMBER] errors on leap for a RNA+Adenine pdb structure zgong.hust (Wed Nov 04 2009 - 06:59:20 CST)
Re: [AMBER] errors on leap for a RNA+Adenine pdb structure FyD (Wed Nov 04 2009 - 07:39:02 CST)
[AMBER] total number of hydrogen bonds of the system as a function of time Markus Kaukonen (Wed Nov 04 2009 - 07:59:17 CST)
Re: [AMBER] total number of hydrogen bonds of the system as a function of time Jason Swails (Wed Nov 04 2009 - 08:08:21 CST)
[AMBER] errors on leap for a RNA+Adenine pdb structure with antechamber zgong.hust (Wed Nov 04 2009 - 09:07:23 CST)
Re: [AMBER] Antechamber and Parmchk problems case (Wed Nov 04 2009 - 09:26:03 CST)
Re: [AMBER] errors on leap for a RNA+Adenine pdb structure with antechamber FyD (Wed Nov 04 2009 - 09:28:04 CST)
Re: [AMBER] AMBER: segmentation fault when running parmchk Alexander Boncheff (Wed Nov 04 2009 - 10:02:50 CST)
Re: [AMBER] AMBER: segmentation fault when running parmchk Mark Williamson (Wed Nov 04 2009 - 11:06:53 CST)
[AMBER] pmemd vs sander.MPI Taufik Al-Sarraj (Wed Nov 04 2009 - 11:32:05 CST)
Re: [AMBER] amber parameter file creation and usage Donald Keidel (Wed Nov 04 2009 - 11:53:23 CST)
RE: [AMBER] pmemd vs sander.MPI Ross Walker (Wed Nov 04 2009 - 12:33:23 CST)
Re: [AMBER] AMBER: segmentation fault when running parmchk Bill Ross (Wed Nov 04 2009 - 12:39:32 CST)
[AMBER] HB for each snapshot Marcin Krol (Wed Nov 04 2009 - 13:14:41 CST)
Re: [AMBER] Antechamber and Parmchk problems Junmei Wang (Wed Nov 04 2009 - 13:21:25 CST)
Re: [AMBER] AMBER: segmentation fault when running parmchk Junmei Wang (Wed Nov 04 2009 - 13:22:54 CST)
Re: [AMBER] HB for each snapshot Jason Swails (Wed Nov 04 2009 - 13:35:07 CST)
Re: Re: [AMBER] Antechamber and Parmchk problems cyk5056 (Wed Nov 04 2009 - 13:56:32 CST)
Re: Re: [AMBER] Antechamber and Parmchk problems cyk5056 (Wed Nov 04 2009 - 14:37:55 CST)
Re: Re: [AMBER] Antechamber and Parmchk problems Junmei Wang (Wed Nov 04 2009 - 15:07:35 CST)
Re: Re: [AMBER] errors on leap for a RNA+Adenine pdb structure withantechamber zgong.hust (Wed Nov 04 2009 - 20:18:52 CST)
Re: [AMBER] RE: question rrd (Wed Nov 04 2009 - 20:52:04 CST)
Re: [AMBER] errors on leap for a RNA+Adenine pdb structure withantechamber FyD (Wed Nov 04 2009 - 23:42:43 CST)
Re: [AMBER] RE: question steinbrt_at_rci.rutgers.edu (Thu Nov 05 2009 - 02:12:47 CST)
Re: [AMBER] HB for each snapshot Nicolas Sapay (Thu Nov 05 2009 - 02:30:51 CST)
[AMBER] Phosphothreonine Beale, John (Thu Nov 05 2009 - 07:03:58 CST)
[AMBER] Calculaiton stop ? xuemeiwang1103 (Thu Nov 05 2009 - 07:11:31 CST)
Re: [AMBER] Phosphothreonine Anselm Horn (Thu Nov 05 2009 - 07:17:59 CST)
Re: [AMBER] RE: question Marek Maly (Thu Nov 05 2009 - 07:28:03 CST)
Re: [AMBER] pmemd vs sander.MPI Marek Maly (Thu Nov 05 2009 - 07:36:39 CST)
Re: [AMBER] pmemd vs sander.MPI Robert Duke (Thu Nov 05 2009 - 07:35:41 CST)
Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Thu Nov 05 2009 - 07:39:59 CST)
Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Jason Swails (Thu Nov 05 2009 - 08:12:39 CST)
Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Thu Nov 05 2009 - 08:38:32 CST)
Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Thu Nov 05 2009 - 08:55:16 CST)
RE: [AMBER] MPI process terminated unexpectedly after cluster upgrade Ross Walker (Thu Nov 05 2009 - 10:22:19 CST)
[AMBER] zeros in excluded atom list in topology file Peter Schmidtke (Thu Nov 05 2009 - 11:06:41 CST)
Re: [AMBER] pmemd vs sander.MPI Marek Maly (Thu Nov 05 2009 - 12:03:08 CST)
[AMBER] Segmentation Fault Beale, John (Thu Nov 05 2009 - 12:04:52 CST)
Re: [AMBER] pmemd vs sander.MPI Robert Duke (Thu Nov 05 2009 - 12:06:24 CST)
RE: [AMBER] pmemd vs sander.MPI Ross Walker (Thu Nov 05 2009 - 12:27:19 CST)
RE: [AMBER] Segmentation Fault Ross Walker (Thu Nov 05 2009 - 12:29:20 CST)
Re: [AMBER] pmemd vs sander.MPI Marek Maly (Thu Nov 05 2009 - 12:34:31 CST)
Re: [AMBER] pmemd vs sander.MPI Marek Maly (Thu Nov 05 2009 - 12:47:06 CST)
Re: Re: Re: [AMBER] Antechamber and Parmchk problems cyk5056 (Thu Nov 05 2009 - 12:59:28 CST)
[AMBER] RESP using antechamber with Se atom Donald Keidel (Thu Nov 05 2009 - 13:21:37 CST)
Re: Re: Re: [AMBER] Antechamber and Parmchk problems Junmei Wang (Thu Nov 05 2009 - 15:16:51 CST)
[AMBER] ff fitting ? Marek Maly (Thu Nov 05 2009 - 15:38:38 CST)
Re: [AMBER] RESP using antechamber with Se atom Junmei Wang (Thu Nov 05 2009 - 15:39:46 CST)
RE: [AMBER] pmemd vs sander.MPI Ross Walker (Thu Nov 05 2009 - 16:58:37 CST)
Re: [AMBER] pmemd vs sander.MPI Marek Maly (Thu Nov 05 2009 - 17:58:50 CST)
Re: [AMBER] RE: question rrd (Thu Nov 05 2009 - 18:09:11 CST)
Re: [AMBER] zeros in excluded atom list in topology file Carlos Simmerling (Thu Nov 05 2009 - 18:39:56 CST)
[AMBER] varying positional restraints with PMEMD Julian Garrec (Thu Nov 05 2009 - 18:43:35 CST)
Re: [AMBER] RESP using antechamber with Se atom subarna thakur (Thu Nov 05 2009 - 23:21:46 CST)
[AMBER] error in kclust of MMTB_tool set kureeckal ramesh (Fri Nov 06 2009 - 01:33:01 CST)
Re: [AMBER] zeros in excluded atom list in topology file Peter Schmidtke (Fri Nov 06 2009 - 02:54:57 CST)
[AMBER] amber9 compilation Myunggi Yi (Fri Nov 06 2009 - 09:10:03 CST)
[AMBER] amber 9 compilation Myunggi Yi (Fri Nov 06 2009 - 09:13:00 CST)
Re: [AMBER] amber9 compilation David Watson (Fri Nov 06 2009 - 09:19:31 CST)
Re: [AMBER] amber9 compilation Myunggi Yi (Fri Nov 06 2009 - 09:50:25 CST)
Re: [AMBER] amber9 compilation David Watson (Fri Nov 06 2009 - 10:16:58 CST)
Re: [AMBER] RESP using antechamber with Se atom Eric Pettersen (Fri Nov 06 2009 - 10:49:16 CST)
[AMBER] -np not 2^x a problem w/ sander??? Dean Cuebas (Fri Nov 06 2009 - 13:27:48 CST)
[AMBER] -np not 2^x a problem w/ sander??? update Dean Cuebas (Fri Nov 06 2009 - 13:46:39 CST)
Re: [AMBER] zeros in excluded atom list in topology file case (Fri Nov 06 2009 - 16:44:04 CST)
Re: [AMBER] zeros in excluded atom list in topology file Peter Schmidtke (Fri Nov 06 2009 - 18:07:44 CST)
Re: [AMBER] zeros in excluded atom list in topology file Bill Ross (Fri Nov 06 2009 - 18:09:39 CST)
[AMBER] unable to find mopac charges in mopac.out Richard Tseng (Fri Nov 06 2009 - 19:14:20 CST)
Re: [AMBER] unable to find mopac charges in mopac.out Bill Ross (Fri Nov 06 2009 - 19:22:22 CST)
RE: [AMBER] -np not 2^x a problem w/ sander??? Ross Walker (Fri Nov 06 2009 - 19:43:04 CST)
[AMBER] ptraj script for H bond for protein (explicit ) kureeckal ramesh (Sat Nov 07 2009 - 01:38:29 CST)
[AMBER] Low frequency Raman spectra babak minoofar (Sat Nov 07 2009 - 06:53:37 CST)
Re: [AMBER] unable to find mopac charges in mopac.out case (Sat Nov 07 2009 - 07:59:43 CST)
[AMBER] the problem of nucgen.dat liangchen88_at_ucla.edu (Sat Nov 07 2009 - 08:41:49 CST)
Re: [AMBER] the problem of nucgen.dat case (Sat Nov 07 2009 - 08:51:57 CST)
Re: [AMBER] Low frequency Raman spectra case (Sat Nov 07 2009 - 09:02:02 CST)
[AMBER] linux version for Amber10 liangchen88_at_ucla.edu (Sat Nov 07 2009 - 09:28:05 CST)
[AMBER] linux version for Amber10 liangchen88_at_ucla.edu (Sat Nov 07 2009 - 09:28:05 CST)
Re: [AMBER] linux version for Amber10 Peter Schmidtke (Sat Nov 07 2009 - 09:58:18 CST)
RE: [AMBER] -np not 2^x a problem w/ sander??? update Ross Walker (Sat Nov 07 2009 - 10:31:36 CST)
[AMBER] build up solvate box Huikuan Chao (Sat Nov 07 2009 - 14:29:50 CST)
[AMBER] sleap fastbld error Oliver Kuhn (Sat Nov 07 2009 - 14:39:29 CST)
[AMBER] sleap fastbld error is not an error Oliver Kuhn (Sat Nov 07 2009 - 15:07:35 CST)
Re: [AMBER]Amber10 + g95 Sudeep Narayan Banerjee (Sat Nov 07 2009 - 20:56:39 CST)
Re: [AMBER] linux version for Amber10 Sudeep Narayan Banerjee (Sat Nov 07 2009 - 20:56:19 CST)
Re: [AMBER] linux version for Amber10 Jason Swails (Sat Nov 07 2009 - 21:38:41 CST)
Re: [AMBER]Amber10 + g95 Abhishek Banerjee (Sat Nov 07 2009 - 21:41:54 CST)
Re: [AMBER] the problem of nucgen.dat liangchen88_at_ucla.edu (Sat Nov 07 2009 - 21:48:54 CST)
Re: [AMBER] linux version for Amber10 liangchen88_at_ucla.edu (Sat Nov 07 2009 - 21:59:53 CST)
[AMBER] LJ parameters for HO and HW manoj singh (Sat Nov 07 2009 - 23:21:22 CST)
Re: [AMBER] LJ parameters for HO and HW Jason Swails (Sat Nov 07 2009 - 23:50:03 CST)
Re: [AMBER] LJ parameters for HO and HW manoj singh (Sun Nov 08 2009 - 00:09:13 CST)
[AMBER] solvent Jio M (Sun Nov 08 2009 - 08:12:34 CST)
[AMBER] MM_PBSA enquiries s. Bill (Sun Nov 08 2009 - 08:53:04 CST)
Re: [AMBER] LJ parameters for HO and HW Jason Swails (Sun Nov 08 2009 - 09:14:45 CST)
Re: [AMBER] MM_PBSA enquiries manoj singh (Sun Nov 08 2009 - 09:21:12 CST)
Re: [AMBER] the problem of nucgen.dat case (Sun Nov 08 2009 - 10:19:03 CST)
[AMBER] pmemd failure Francesco Pietra (Sun Nov 08 2009 - 10:52:28 CST)
Re: [AMBER] pmemd failure Robert Duke (Sun Nov 08 2009 - 11:00:52 CST)
[AMBER] Gly -> Ala mutation manoj singh (Sun Nov 08 2009 - 11:25:46 CST)
Re: [AMBER] varying positional restraints with PMEMD case (Sun Nov 08 2009 - 11:37:53 CST)
Re: [AMBER] ff fitting ? case (Sun Nov 08 2009 - 11:42:42 CST)
Re: [AMBER] Gly -> Ala mutation Jason Swails (Sun Nov 08 2009 - 11:53:29 CST)
Re: [AMBER] pmemd failure Francesco Pietra (Sun Nov 08 2009 - 13:08:53 CST)
Re: [AMBER] Gly -> Ala mutation manoj singh (Sun Nov 08 2009 - 13:14:23 CST)
Re: [AMBER] Gly -> Ala mutation Jason Swails (Sun Nov 08 2009 - 14:16:42 CST)
Re: [AMBER] Gly -> Ala mutation manoj singh (Sun Nov 08 2009 - 15:18:37 CST)
[AMBER] error in kclust of MMTB_tool set kureeckal ramesh (Sun Nov 08 2009 - 18:10:58 CST)
[AMBER] analyzeMatrix: cannot find a match in the matrixInfoStack Naser Alijabbari (Sun Nov 08 2009 - 19:43:56 CST)
[AMBER] conversion of kelvin to kcal/mol aneesh cna (Sun Nov 08 2009 - 23:08:33 CST)
Re: [AMBER] conversion of kelvin to kcal/mol manoj singh (Sun Nov 08 2009 - 23:17:03 CST)
Re: [AMBER] conversion of kelvin to kcal/mol aneesh cna (Mon Nov 09 2009 - 00:56:36 CST)
Re: [AMBER] LJ parameters for HO and HW steinbrt_at_rci.rutgers.edu (Mon Nov 09 2009 - 02:23:20 CST)
[AMBER] sander.mpi. mdfil: Error unknown flag: sander Andrew Voronkov (Mon Nov 09 2009 - 06:24:17 CST)
Re: [AMBER] ff fitting ? Marek Maly (Mon Nov 09 2009 - 06:38:35 CST)
[AMBER] Task is running on supercomputer without any output Andrew Voronkov (Mon Nov 09 2009 - 06:39:36 CST)
Re: [AMBER] Task is running on supercomputer without any output michael bane (Mon Nov 09 2009 - 06:51:17 CST)
Re: [AMBER] sander.mpi. mdfil: Error unknown flag: sander case (Mon Nov 09 2009 - 07:17:23 CST)
Re: [AMBER] Gly -> Ala mutation Carlos Simmerling (Mon Nov 09 2009 - 09:13:08 CST)
Re: [AMBER] Gly -> Ala mutation manoj singh (Mon Nov 09 2009 - 10:10:40 CST)
Re: [AMBER] Gly -> Ala mutation Adrian Roitberg (Mon Nov 09 2009 - 10:13:11 CST)
Re: [AMBER] Gly -> Ala mutation manoj singh (Mon Nov 09 2009 - 10:26:00 CST)
Re: [AMBER] unable to find mopac charges in mopac.out Richard Tseng (Mon Nov 09 2009 - 10:39:51 CST)
Re: [AMBER] unable to find mopac charges in mopac.out case (Mon Nov 09 2009 - 10:47:01 CST)
[AMBER] PCA analysis with ptraj Alessandro Contini (Mon Nov 09 2009 - 11:00:19 CST)
Re: [AMBER] LJ parameters for HO and HW Bill Ross (Mon Nov 09 2009 - 11:29:40 CST)
[AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Mon Nov 09 2009 - 13:14:25 CST)
Re: [AMBER] unable to find mopac charges in mopac.out Richard Tseng (Mon Nov 09 2009 - 13:25:11 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala David Watson (Mon Nov 09 2009 - 13:28:31 CST)
[AMBER] Getting minimized .pdb file without non-polar hydrogens Francesco Pietra (Mon Nov 09 2009 - 13:31:40 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case (Mon Nov 09 2009 - 14:02:42 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Mark Williamson (Mon Nov 09 2009 - 14:14:03 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case (Mon Nov 09 2009 - 14:41:59 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Mon Nov 09 2009 - 16:05:32 CST)
[AMBER] rectangular box with PME problem Ivan Gladich (Mon Nov 09 2009 - 16:18:16 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala David Watson (Mon Nov 09 2009 - 16:35:32 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala David Watson (Mon Nov 09 2009 - 18:25:12 CST)
RE: [AMBER] PCA analysis with ptraj hannes.loeffler_at_stfc.ac.uk (Tue Nov 10 2009 - 02:13:29 CST)
[AMBER] three trials to create topologies with sleap and tleap Oliver Kuhn (Tue Nov 10 2009 - 03:34:36 CST)
RE: [AMBER] PCA analysis with ptraj Alessandro Contini (Tue Nov 10 2009 - 06:03:48 CST)
[AMBER] error in kclust of MMTB_tool set kureeckal ramesh (Tue Nov 10 2009 - 06:41:31 CST)
[AMBER] MMTSB tool set PDF kureeckal ramesh (Tue Nov 10 2009 - 08:02:39 CST)
[AMBER] matrixinfoStack Naser Alijabbari (Tue Nov 10 2009 - 08:45:12 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Tue Nov 10 2009 - 09:41:18 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case (Tue Nov 10 2009 - 10:28:17 CST)
[AMBER] error reading namelist cntrl Shaikh Abdul R S Ramaju (Wed Nov 11 2009 - 00:51:45 CST)
[AMBER] coarse-grained MD Francesco Pietra (Wed Nov 11 2009 - 02:27:27 CST)
[AMBER] Creating new residue with tleap. rrd (Wed Nov 11 2009 - 05:02:23 CST)
Re: [AMBER] Creating new residue with tleap. case (Wed Nov 11 2009 - 06:37:47 CST)
Re: [AMBER] error reading namelist cntrl Jason Swails (Wed Nov 11 2009 - 08:01:42 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Wed Nov 11 2009 - 08:17:42 CST)
[AMBER] Increase Temperature to 550 K Chih-Ying Lin (Wed Nov 11 2009 - 09:27:41 CST)
[AMBER] High-temperature simulation ? Chih-Ying Lin (Wed Nov 11 2009 - 09:36:16 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Giorgio Maccari (Wed Nov 11 2009 - 10:53:04 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala David Watson (Wed Nov 11 2009 - 10:56:01 CST)
Re: [AMBER] High-temperature simulation ? Carlos Simmerling (Wed Nov 11 2009 - 11:26:15 CST)
Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling (Wed Nov 11 2009 - 11:52:55 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Bill Ross (Wed Nov 11 2009 - 11:54:01 CST)
Re: [AMBER] Increase Temperature to 550 K Chih-Ying Lin (Wed Nov 11 2009 - 15:08:12 CST)
Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling (Wed Nov 11 2009 - 15:14:24 CST)
[AMBER] Lisp library for amber analysis? Eric Shamay (Wed Nov 11 2009 - 15:54:12 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Wed Nov 11 2009 - 16:04:28 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Jason Swails (Wed Nov 11 2009 - 16:30:35 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case (Wed Nov 11 2009 - 16:36:59 CST)
Re: [AMBER] Increase Temperature to 550 K FyD (Thu Nov 12 2009 - 01:51:24 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Thu Nov 12 2009 - 02:15:40 CST)
RE: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Ross Walker (Thu Nov 12 2009 - 04:52:44 CST)
[AMBER] reg. GBA balaji nagarajan (Thu Nov 12 2009 - 06:06:30 CST)
Re: [AMBER] Increase Temperature to 550 K case (Thu Nov 12 2009 - 06:55:18 CST)
Re: [AMBER] reg. GBA case (Thu Nov 12 2009 - 07:02:43 CST)
[AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov (Thu Nov 12 2009 - 07:23:22 CST)
Re: [AMBER] Task is running on supercomputer without any output Andrew Voronkov (Thu Nov 12 2009 - 07:24:56 CST)
Re: [AMBER] MD snapshots of most probable protein conformations in Amber Adrian Roitberg (Thu Nov 12 2009 - 07:30:53 CST)
Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling (Thu Nov 12 2009 - 08:22:08 CST)
[AMBER] MM_PBSA energy per residue Hemant Kumar (Thu Nov 12 2009 - 08:27:22 CST)
Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Thu Nov 12 2009 - 10:05:03 CST)
[AMBER] slope Jio M (Thu Nov 12 2009 - 13:28:02 CST)
[AMBER] R.E.D. resp error s. Bill (Thu Nov 12 2009 - 14:23:31 CST)
Re: [AMBER] Increase Temperature to 550 K Chih-Ying Lin (Thu Nov 12 2009 - 15:59:11 CST)
Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling (Thu Nov 12 2009 - 16:29:13 CST)
Re: [AMBER] Increase Temperature to 550 K Chih-Ying Lin (Thu Nov 12 2009 - 22:36:07 CST)
Re: [AMBER] R.E.D. resp error FyD (Thu Nov 12 2009 - 23:36:44 CST)
[AMBER] R.E.D. too small charges Andrei Neamtu (Fri Nov 13 2009 - 02:57:04 CST)
Re: [AMBER] Increase Temperature to 550 K FyD (Fri Nov 13 2009 - 05:43:48 CST)
Re: [AMBER] R.E.D. too small charges FyD (Fri Nov 13 2009 - 07:06:51 CST)
[AMBER] enquiry regarding parameter file to be used bharat lakhani (Fri Nov 13 2009 - 07:35:30 CST)
Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling (Fri Nov 13 2009 - 07:35:28 CST)
Re: [AMBER] enquiry regarding parameter file to be used Carlos Simmerling (Fri Nov 13 2009 - 07:41:50 CST)
[AMBER] matrixInfoStack Naser Alijabbari (Fri Nov 13 2009 - 08:52:52 CST)
[AMBER] request sculiujl (Fri Nov 13 2009 - 20:59:22 CST)
[AMBER] the different RMSD? qiaoyan (Fri Nov 13 2009 - 21:37:36 CST)
Re: [AMBER] the different RMSD? Thomas Cheatham (Fri Nov 13 2009 - 21:40:56 CST)
Re: Re: [AMBER] the different RMSD? qiaoyan (Fri Nov 13 2009 - 22:16:27 CST)
[AMBER] is rst file the last structure? qiaoyan (Fri Nov 13 2009 - 22:52:40 CST)
Re: [AMBER] enquiry regarding parameter file to be used bharat lakhani (Fri Nov 13 2009 - 23:52:58 CST)
[AMBER] Hydrogen bond analysis for protein dna complex using ptraj shamoon siddiqui (Sat Nov 14 2009 - 09:56:04 CST)
Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj Carlos Simmerling (Sat Nov 14 2009 - 10:00:39 CST)
Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj shamoon siddiqui (Sat Nov 14 2009 - 10:19:04 CST)
Re: Re: [AMBER] the different RMSD? Thomas Cheatham (Sat Nov 14 2009 - 10:25:43 CST)
Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj Thomas Cheatham (Sat Nov 14 2009 - 11:06:15 CST)
Re: [AMBER] is rst file the last structure? Jason Swails (Sat Nov 14 2009 - 11:18:22 CST)
Re: Re: Re: [AMBER] the different RMSD? qiaoyan (Sat Nov 14 2009 - 20:02:53 CST)
Re: [AMBER] is rst file the last structure? case (Sun Nov 15 2009 - 08:33:16 CST)
[AMBER] How to split mdcrd files shamoon siddiqui (Sun Nov 15 2009 - 11:22:52 CST)
Re: [AMBER] How to split mdcrd files Carlos Simmerling (Sun Nov 15 2009 - 11:28:06 CST)
Re: [AMBER] How to split mdcrd files Jason Swails (Sun Nov 15 2009 - 11:35:24 CST)
Re: [AMBER] How to split mdcrd files Carlos Simmerling (Sun Nov 15 2009 - 11:56:48 CST)
[AMBER] slope {no reply} Jio M (Sun Nov 15 2009 - 13:03:17 CST)
Re: [AMBER] slope {no reply} Carlos Simmerling (Sun Nov 15 2009 - 13:07:02 CST)
Re: [AMBER] How to split mdcrd files Thomas Cheatham (Sun Nov 15 2009 - 15:06:34 CST)
Re: [AMBER] slope Jio M (Sun Nov 15 2009 - 22:42:52 CST)
[AMBER] Etot positive Jio M (Sun Nov 15 2009 - 23:06:22 CST)
Re: [AMBER] slope Carlos Simmerling (Mon Nov 16 2009 - 05:11:46 CST)
Re: [AMBER] Etot positive Carlos Simmerling (Mon Nov 16 2009 - 05:13:55 CST)
Re: [AMBER] enquiry regarding parameter file to be used Carlos Simmerling (Mon Nov 16 2009 - 05:40:49 CST)
[AMBER] Segmentation fault in antechamber albert albert (Mon Nov 16 2009 - 09:28:20 CST)
Re: [AMBER] Segmentation fault in antechamber case (Mon Nov 16 2009 - 09:53:30 CST)
Re: [AMBER] Segmentation fault in antechamber albert albert (Mon Nov 16 2009 - 10:23:02 CST)
[AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin (Mon Nov 16 2009 - 10:43:18 CST)
Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Mark Williamson (Mon Nov 16 2009 - 11:37:18 CST)
Re: [AMBER] slope {no reply} Bill Ross (Mon Nov 16 2009 - 11:48:22 CST)
Re: [AMBER] Segmentation fault in antechamber Mark Williamson (Mon Nov 16 2009 - 11:48:32 CST)
Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin (Mon Nov 16 2009 - 13:07:20 CST)
Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Mark Williamson (Mon Nov 16 2009 - 13:49:58 CST)
RE: [AMBER] Etot positive Ross Walker (Mon Nov 16 2009 - 20:50:02 CST)
Re: [AMBER] slope Jio M (Mon Nov 16 2009 - 22:07:07 CST)
[AMBER] Re:Etot positive Jio M (Mon Nov 16 2009 - 22:59:26 CST)
Re: [AMBER] slope {no reply} Jio M (Mon Nov 16 2009 - 23:13:44 CST)
[AMBER] compilation problem of amber9 sculiujl (Tue Nov 17 2009 - 01:03:22 CST)
[AMBER] compilation problem of amber sculiujl (Tue Nov 17 2009 - 01:33:52 CST)
[AMBER] which is the best intel complier for amber 10? jacky zhao (Tue Nov 17 2009 - 02:24:30 CST)
Re: [AMBER]Amber10 + g95 jacky zhao (Tue Nov 17 2009 - 02:26:56 CST)
[AMBER] About zinc parameters ? xuemeiwang1103 (Tue Nov 17 2009 - 02:52:56 CST)
Re: [AMBER] About zinc parameters ? steinbrt_at_rci.rutgers.edu (Tue Nov 17 2009 - 04:35:24 CST)
Re: [AMBER] slope Carlos Simmerling (Tue Nov 17 2009 - 05:10:35 CST)
Re: [AMBER] slope {no reply} Carlos Simmerling (Tue Nov 17 2009 - 05:11:23 CST)
Re: [AMBER] compilation problem of amber Jason Swails (Tue Nov 17 2009 - 08:51:42 CST)
Re: [AMBER] compilation problem of amber9 Jason Swails (Tue Nov 17 2009 - 08:55:46 CST)
Re: [AMBER] About zinc parameters ? Jason Swails (Tue Nov 17 2009 - 09:17:23 CST)
Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin (Tue Nov 17 2009 - 09:20:13 CST)
[AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Tue Nov 17 2009 - 09:47:12 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Jason Swails (Tue Nov 17 2009 - 09:57:41 CST)
RE: [AMBER] non standart residue library creation with tleap (Zn atom) intra\\sa175950 (Tue Nov 17 2009 - 10:18:38 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Tue Nov 17 2009 - 10:34:33 CST)
[AMBER] tleap maximum coordination exceeded Jack Shultz (Tue Nov 17 2009 - 10:52:20 CST)
Re: [AMBER] Segmentation fault in antechamber albert albert (Tue Nov 17 2009 - 11:04:46 CST)
Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala case (Tue Nov 17 2009 - 11:29:42 CST)
Re: [AMBER] About zinc parameters ? Sally Pias (Tue Nov 17 2009 - 11:38:29 CST)
Re: [AMBER] slope {no reply} Bill Ross (Tue Nov 17 2009 - 11:51:08 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Jason Swails (Tue Nov 17 2009 - 12:05:05 CST)
[AMBER] MSD of ligand?? Chih-Ying Lin (Tue Nov 17 2009 - 13:07:12 CST)
Re: [AMBER] slope {no reply} Jio M (Tue Nov 17 2009 - 13:13:06 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Tue Nov 17 2009 - 14:10:03 CST)
Re: [AMBER] tleap maximum coordination exceeded FyD (Tue Nov 17 2009 - 14:18:20 CST)
Re: [AMBER] tleap maximum coordination exceeded case (Tue Nov 17 2009 - 14:24:09 CST)
[AMBER] combining parameter files of ligand and enzyme Amire-Brahimi Benjamin (Tue Nov 17 2009 - 16:31:32 CST)
Re: [AMBER] slope {no reply} Carlos Simmerling (Tue Nov 17 2009 - 17:49:39 CST)
Re: [AMBER] slope {no reply} Bill Ross (Tue Nov 17 2009 - 19:04:48 CST)
Re: [AMBER] tleap maximum coordination exceeded Jack Shultz (Tue Nov 17 2009 - 19:51:38 CST)
[AMBER] have a question jacky zhao (Tue Nov 17 2009 - 19:54:36 CST)
Re: [AMBER] have a question Bill Ross (Tue Nov 17 2009 - 20:02:45 CST)
[AMBER] the different RMSD? qiaoyan (Tue Nov 17 2009 - 20:47:42 CST)
Re: [AMBER] tleap maximum coordination exceeded Jack Shultz (Tue Nov 17 2009 - 21:05:41 CST)
Re: [AMBER] Segmentation fault in antechamber case (Tue Nov 17 2009 - 22:28:14 CST)
[AMBER] How to change the input matrix for "analyze matrix" instruction? cyk5056 (Tue Nov 17 2009 - 22:37:43 CST)
[AMBER] Can I get an average trajectory? cyk5056 (Tue Nov 17 2009 - 22:46:25 CST)
Re: [AMBER] tleap maximum coordination exceeded case (Tue Nov 17 2009 - 22:45:55 CST)
Re: [AMBER] slope {no reply} Jio M (Tue Nov 17 2009 - 23:09:34 CST)
å›žå¤ï¼š [AMBER] the different RMSD? Rilei Yu (Tue Nov 17 2009 - 23:25:17 CST)
Re: [AMBER] combining parameter files of ligand and enzyme FyD (Wed Nov 18 2009 - 01:49:23 CST)
[AMBER] GB and Atom Type Alexander Seifert (Wed Nov 18 2009 - 02:58:32 CST)
Re: [AMBER] Can I get an average trajectory? Carlos Simmerling (Wed Nov 18 2009 - 06:08:59 CST)
[AMBER] Asking help for parallel installation of Amber9 nicholus bhattacharjee (Wed Nov 18 2009 - 06:27:03 CST)
Re: [AMBER] Asking help for parallel installation of Amber9 David Watson (Wed Nov 18 2009 - 06:36:03 CST)
Re: [AMBER] Asking help for parallel installation of Amber9 nicholus bhattacharjee (Wed Nov 18 2009 - 07:00:36 CST)
Re: [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov (Wed Nov 18 2009 - 07:09:52 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Wed Nov 18 2009 - 07:19:58 CST)
Re: [AMBER] Asking help for parallel installation of Amber9 David Watson (Wed Nov 18 2009 - 07:23:17 CST)
[AMBER] read substrate into leap sculiujl (Wed Nov 18 2009 - 07:37:19 CST)
Re: [AMBER] MD snapshots of most probable protein conformations in Amber Renata KWIECIEN (Wed Nov 18 2009 - 07:39:52 CST)
Re: [AMBER] MD snapshots of most probable protein conformations in Amber Carlos Simmerling (Wed Nov 18 2009 - 07:53:14 CST)
Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin (Wed Nov 18 2009 - 08:21:57 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Wed Nov 18 2009 - 08:29:14 CST)
Re: [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov (Wed Nov 18 2009 - 09:32:11 CST)
Re: [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov (Wed Nov 18 2009 - 09:33:54 CST)
Re: Re: [AMBER] Can I get an average trajectory? cyk5056 (Wed Nov 18 2009 - 10:02:38 CST)
Re:[AMBER] How to change the input matrix for "analyze matrix" instruction? ³ÂÒ»Ù© (Wed Nov 18 2009 - 10:18:51 CST)
[AMBER] about divcon Alan (Wed Nov 18 2009 - 10:24:51 CST)
Re: [AMBER] about divcon case (Wed Nov 18 2009 - 10:53:16 CST)
Re: [AMBER] about divcon Alan (Wed Nov 18 2009 - 11:07:44 CST)
Re: [AMBER] MD snapshots of most probable protein conformations in Amber Carlos Simmerling (Wed Nov 18 2009 - 11:14:50 CST)
Re: [AMBER] Asking help for parallel installation of Amber9 Bill Ross (Wed Nov 18 2009 - 11:48:51 CST)
Re: [AMBER] Asking help for parallel installation of Amber9 David Watson (Wed Nov 18 2009 - 12:04:38 CST)
Re: [AMBER] read substrate into leap Jason Swails (Wed Nov 18 2009 - 12:53:30 CST)
Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Jason Swails (Wed Nov 18 2009 - 13:00:09 CST)
Re: [AMBER] about divcon Jason Swails (Wed Nov 18 2009 - 13:09:43 CST)
[AMBER] The decreasing MSD of ligand?? Chih-Ying Lin (Wed Nov 18 2009 - 15:19:35 CST)
[AMBER] Is the integral value from RDF the same as average number of atoms? Gustaf Olsson (go22bi_at_student.hik.se) (Wed Nov 18 2009 - 15:56:31 CST)
Re:Re: [AMBER] read substrate into leap sculiujl (Wed Nov 18 2009 - 19:12:13 CST)
Re: Re: [AMBER] read substrate into leap Jason Swails (Wed Nov 18 2009 - 19:35:37 CST)
Re:Re: [AMBER] read substrate into leap Bill Ross (Wed Nov 18 2009 - 19:59:33 CST)
Re: [AMBER] GB and Atom Type Sally Pias (Wed Nov 18 2009 - 23:11:27 CST)
Re: [AMBER] slope {no reply} Sally Pias (Wed Nov 18 2009 - 23:39:53 CST)
Re: [AMBER] slope {no reply} Jio M (Thu Nov 19 2009 - 11:15:25 CST)
[AMBER] AmberTools 1.3 has a likely release date? Alan (Thu Nov 19 2009 - 12:15:30 CST)
[AMBER] implicit_run_error balaji nagarajan (Thu Nov 19 2009 - 12:37:21 CST)
[AMBER] The MSD and periodic boundary condition Chih-Ying Lin (Thu Nov 19 2009 - 17:30:46 CST)
Re: [AMBER] The MSD and periodic boundary condition Jason Swails (Thu Nov 19 2009 - 18:00:30 CST)
[AMBER] errors on leap for a RNA + Non-Standard molecule pdb structure Yunjie Zhao (Thu Nov 19 2009 - 22:37:34 CST)
Re: [AMBER] enquiry regarding parameter file to be used bharat lakhani (Thu Nov 19 2009 - 23:35:14 CST)
Re: [AMBER] enquiry regarding parameter file to be used Carlos Simmerling (Fri Nov 20 2009 - 05:20:05 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Fri Nov 20 2009 - 05:35:31 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) case (Fri Nov 20 2009 - 07:30:54 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Fri Nov 20 2009 - 07:42:58 CST)
Re: [AMBER] AmberTools 1.3 has a likely release date? case (Fri Nov 20 2009 - 08:50:23 CST)
Re: [AMBER] implicit_run_error case (Fri Nov 20 2009 - 08:53:31 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Fri Nov 20 2009 - 09:07:26 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Fri Nov 20 2009 - 09:25:30 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Fri Nov 20 2009 - 09:40:50 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Fri Nov 20 2009 - 10:02:57 CST)
[AMBER] rmsd Taufik Al-Sarraj (Fri Nov 20 2009 - 10:32:24 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Fri Nov 20 2009 - 11:47:00 CST)
[AMBER] standard way to upload a lipid bilayer Syed Kashif Zafar (Sat Nov 21 2009 - 05:40:08 CST)
Re: [AMBER] standard way to upload a lipid bilayer David Watson (Sat Nov 21 2009 - 07:06:29 CST)
Re: [AMBER] rmsd Thomas Cheatham (Sat Nov 21 2009 - 15:44:41 CST)
[AMBER] looking for parameters for DHFR substrates and inhibitors... Sidney Elmer (Sat Nov 21 2009 - 22:47:50 CST)
Re: [AMBER] slope {no reply} Sally Pias (Sun Nov 22 2009 - 00:53:39 CST)
[AMBER] NAD - mmpbsa Urszula Uciechowska (Sun Nov 22 2009 - 05:02:22 CST)
[AMBER] Polarizable simulation of the slab Jan Heyda (Sun Nov 22 2009 - 07:13:16 CST)
[AMBER] Fortran error in standard simulation Oliver Kuhn (Mon Nov 23 2009 - 03:26:30 CST)
[AMBER] Fortran error in standard simulation 2 Oliver Kuhn (Mon Nov 23 2009 - 03:34:21 CST)
[AMBER] Fortran error in standard simulation 3 Oliver Kuhn (Mon Nov 23 2009 - 03:47:44 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Mon Nov 23 2009 - 06:35:55 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Mon Nov 23 2009 - 07:25:15 CST)
[AMBER] matrixInfoStack Naser Alijabbari (Mon Nov 23 2009 - 08:42:43 CST)
Re: [AMBER] Segmentation fault in antechamber albert albert (Mon Nov 23 2009 - 09:23:00 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Mon Nov 23 2009 - 09:44:45 CST)
[AMBER] hbond analysis by ptraj- segmentation fault Jayalakshmi Sridhar (Mon Nov 23 2009 - 09:51:00 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Mon Nov 23 2009 - 10:06:01 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Mon Nov 23 2009 - 10:35:51 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Mon Nov 23 2009 - 11:22:23 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Mon Nov 23 2009 - 11:31:31 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Mon Nov 23 2009 - 11:38:28 CST)
Re: [AMBER] hbond analysis by ptraj- segmentation fault Daniel Roe (Mon Nov 23 2009 - 11:42:49 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Mon Nov 23 2009 - 11:49:05 CST)
Re: [AMBER] hbond analysis by ptraj- segmentation fault Daniel Roe (Mon Nov 23 2009 - 11:49:23 CST)
Re: [AMBER] hbond analysis by ptraj- segmentation fault Jayalakshmi Sridhar (Mon Nov 23 2009 - 12:36:25 CST)
Re: [AMBER] rmsd Taufik Al-Sarraj (Mon Nov 23 2009 - 13:24:49 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Mon Nov 23 2009 - 13:50:42 CST)
[AMBER] Regarding Urey-Bradley term in amber calculation aneesh cna (Tue Nov 24 2009 - 00:48:04 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Tue Nov 24 2009 - 02:40:42 CST)
[AMBER] How to get total energy of asystem gunajyoti das (Tue Nov 24 2009 - 03:14:06 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Tue Nov 24 2009 - 03:26:37 CST)
Re: [AMBER] How to get total energy of asystem steinbrt_at_rci.rutgers.edu (Tue Nov 24 2009 - 03:43:06 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Tue Nov 24 2009 - 04:12:53 CST)
Re: [AMBER] How to get total energy of asystem case (Tue Nov 24 2009 - 06:36:30 CST)
Re: [AMBER] Regarding Urey-Bradley term in amber calculation Jason Swails (Tue Nov 24 2009 - 06:48:31 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Tue Nov 24 2009 - 08:16:54 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Tue Nov 24 2009 - 08:57:30 CST)
RE: [AMBER] Fortran error in standard simulation Ross Walker (Tue Nov 24 2009 - 10:21:33 CST)
RE: [AMBER] non standart residue library creation with tleap (Zn atom) Ross Walker (Tue Nov 24 2009 - 10:28:21 CST)
RE: [AMBER] non standart residue library creation with tleap (Zn atom) Ross Walker (Tue Nov 24 2009 - 10:29:42 CST)
[AMBER] Hbond analysis output giving no hbonds Jayalakshmi Sridhar (Tue Nov 24 2009 - 10:32:41 CST)
RE: [AMBER] Regarding Urey-Bradley term in amber calculation Ross Walker (Tue Nov 24 2009 - 10:36:49 CST)
RE: [AMBER] Hbond analysis output giving no hbonds Thomas Cheatham (Tue Nov 24 2009 - 10:58:27 CST)
RE: [AMBER] Hbond analysis output giving no hbonds Jayalakshmi Sridhar (Tue Nov 24 2009 - 11:52:47 CST)
Re: [AMBER] non standart residue library creation with tleap (Zn atom) Bill Ross (Tue Nov 24 2009 - 12:09:45 CST)
[AMBER] trouble with antechamber Jennifer L. Muzyka (Tue Nov 24 2009 - 14:13:46 CST)
Re: [AMBER] trouble with antechamber case (Tue Nov 24 2009 - 14:41:24 CST)
[AMBER] how to use amber to verify the reason for difference in affinity Josmar R. da Rocha (Tue Nov 24 2009 - 16:01:34 CST)
[AMBER] check MAXPR in locmem.f error on minimization Jodi Hadden (Tue Nov 24 2009 - 17:46:03 CST)
[AMBER] MM-PBSA NMODE Zhongjie Liang (Tue Nov 24 2009 - 21:12:38 CST)
[AMBER] i-APBS and apbs Rilei Yu (Tue Nov 24 2009 - 23:14:18 CST)
Re: [AMBER] i-APBS and apbs Robert Konecny (Tue Nov 24 2009 - 23:33:37 CST)
Re: [AMBER] i-APBS and apbs Jason Swails (Tue Nov 24 2009 - 23:33:31 CST)
[AMBER] Not able to compile pmemd with openmpi in Amber9 Kito (Wed Nov 25 2009 - 00:39:42 CST)
[AMBER] MM-PB/GBSA NMODE Zhongjie Liang (Wed Nov 25 2009 - 00:50:50 CST)
Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Jason Swails (Wed Nov 25 2009 - 01:06:14 CST)
Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Kito (Wed Nov 25 2009 - 01:11:00 CST)
Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Kito (Wed Nov 25 2009 - 01:50:25 CST)
Re: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Kito (Wed Nov 25 2009 - 02:12:51 CST)
Re: [AMBER] i-APBS and apbs Rilei Yu (Wed Nov 25 2009 - 05:14:15 CST)
Re: [AMBER] check MAXPR in locmem.f error on minimization case (Wed Nov 25 2009 - 07:29:41 CST)
Re: [AMBER] MM-PBSA NMODE case (Wed Nov 25 2009 - 07:31:28 CST)
[AMBER] heme (united-atom) Simon Becker (Wed Nov 25 2009 - 10:30:51 CST)
Re: [AMBER] heme (united-atom) case (Wed Nov 25 2009 - 10:39:10 CST)
Re: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Jason Swails (Wed Nov 25 2009 - 10:50:41 CST)
[AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li (Wed Nov 25 2009 - 11:05:55 CST)
Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Carlos Simmerling (Wed Nov 25 2009 - 11:10:56 CST)
[AMBER] Re: Verlet update time in explicit water Replica Exchange MD Da-Wei Li (Wed Nov 25 2009 - 11:12:23 CST)
Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li (Wed Nov 25 2009 - 11:14:17 CST)
Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li (Wed Nov 25 2009 - 11:28:27 CST)
Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Robert Duke (Wed Nov 25 2009 - 11:38:24 CST)
Re: [AMBER] check MAXPR in locmem.f error on minimization Jodi Hadden (Wed Nov 25 2009 - 12:29:51 CST)
Re: [AMBER] check MAXPR in locmem.f error on minimization Jason Swails (Wed Nov 25 2009 - 12:50:43 CST)
Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li (Wed Nov 25 2009 - 13:43:58 CST)
RE: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Ross Walker (Wed Nov 25 2009 - 14:24:23 CST)
RE: [AMBER] Verlet update time in explicit water Replica Exchange MD Ross Walker (Wed Nov 25 2009 - 14:29:03 CST)
Re: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 case (Wed Nov 25 2009 - 15:06:53 CST)
Re: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Robert Duke (Wed Nov 25 2009 - 16:48:21 CST)
[AMBER] difference between two inputs Jio M (Thu Nov 26 2009 - 00:32:12 CST)
[AMBER] rings getting planar Jio M (Thu Nov 26 2009 - 03:33:09 CST)
[AMBER] ligand parameterization Nahoum Anthony (Thu Nov 26 2009 - 04:49:51 CST)
Re: [AMBER] heme (united-atom) Simon Becker (Thu Nov 26 2009 - 08:34:59 CST)
Re: [AMBER] rings getting planar Jio M (Thu Nov 26 2009 - 08:40:34 CST)
Re: [AMBER] rings getting planar case (Thu Nov 26 2009 - 09:07:43 CST)
Re: [AMBER] ligand parameterization case (Thu Nov 26 2009 - 09:09:05 CST)
Re: [AMBER] ligand parameterization Jason Swails (Thu Nov 26 2009 - 09:47:58 CST)
[AMBER] Atomic radii assignment for WAT molecules DIMAS SUAREZ RODRIGUEZ (Thu Nov 26 2009 - 10:43:33 CST)
RE: [AMBER] ligand parameterization Nahoum Anthony (Thu Nov 26 2009 - 11:19:47 CST)
[AMBER] Polarizable simulation of the slab Jan Heyda (Thu Nov 26 2009 - 12:20:52 CST)
Re: [AMBER] ligand parameterization Jason Swails (Thu Nov 26 2009 - 16:12:34 CST)
Re: [AMBER] ligand parameterization Ilyas Yildirim (Thu Nov 26 2009 - 18:13:09 CST)
[AMBER] MM_PBSA error Jagdeesh C (Thu Nov 26 2009 - 22:28:44 CST)
[AMBER] Re: MM_PBSA error Jagdeesh C (Fri Nov 27 2009 - 03:20:27 CST)
Re: [AMBER] Re: MM_PBSA error Mengjuei Hsieh (Fri Nov 27 2009 - 03:39:54 CST)
Re: [AMBER] Re: MM_PBSA error Jagdeesh C (Fri Nov 27 2009 - 04:13:36 CST)
Re: [AMBER] Polarizable simulation of the slab case (Fri Nov 27 2009 - 08:24:41 CST)
Re: [AMBER] check MAXPR in locmem.f error on minimization Robert Duke (Fri Nov 27 2009 - 08:44:36 CST)
Re: [AMBER] Polarizable simulation of the slab Jan Heyda (Fri Nov 27 2009 - 08:53:57 CST)
Re: [AMBER] difference between two inputs case (Fri Nov 27 2009 - 08:59:01 CST)
Re: [AMBER] Polarizable simulation of the slab case (Fri Nov 27 2009 - 10:10:38 CST)
Re: [AMBER] Polarizable simulation of the slab Jan Heyda (Fri Nov 27 2009 - 10:27:13 CST)
Re: [AMBER] Polarizable simulation of the slab Robert Duke (Fri Nov 27 2009 - 10:48:07 CST)
[AMBER] Regarding rigid bond aneesh cna (Fri Nov 27 2009 - 11:29:15 CST)
Re: [AMBER] Regarding rigid bond Carlos Simmerling (Fri Nov 27 2009 - 12:24:35 CST)
[AMBER] LYS-ASP s. Bill (Fri Nov 27 2009 - 15:47:28 CST)
Re: [AMBER] LYS-ASP Jason Swails (Fri Nov 27 2009 - 19:25:33 CST)
Re: [AMBER] LYS-ASP case (Fri Nov 27 2009 - 21:08:58 CST)
Re: [AMBER] Re: MM_PBSA error Ray Luo (Sat Nov 28 2009 - 12:07:26 CST)
Re: [AMBER] Atomic radii assignment for WAT molecules Ray Luo (Sat Nov 28 2009 - 12:13:42 CST)
[AMBER] where to get leaprc.ff99sb? Jack Shultz (Sat Nov 28 2009 - 18:20:03 CST)
Re: [AMBER] where to get leaprc.ff99sb? Jason Swails (Sat Nov 28 2009 - 19:39:20 CST)
Re: [AMBER] where to get leaprc.ff99sb? Jack Shultz (Sat Nov 28 2009 - 21:19:33 CST)
[AMBER] Scripting tleap Jack Shultz (Sat Nov 28 2009 - 21:42:00 CST)
Re: [AMBER] Scripting tleap Tom Joseph (Sat Nov 28 2009 - 21:45:40 CST)
Re: [AMBER] where to get leaprc.ff99sb? Jason Swails (Sat Nov 28 2009 - 21:51:39 CST)
Re: [AMBER] Scripting tleap Jack Shultz (Sat Nov 28 2009 - 21:54:25 CST)
[AMBER] How to compile and recompile ptraj? cyk5056 (Sun Nov 29 2009 - 16:06:55 CST)
[AMBER] Re: How to compile and recompile ptraj? cyk5056 (Sun Nov 29 2009 - 16:53:37 CST)
Re: [AMBER] Re: How to compile and recompile ptraj? case (Sun Nov 29 2009 - 19:41:24 CST)
Re: [AMBER] how to use amber to verify the reason for difference in affinity case (Sun Nov 29 2009 - 20:55:38 CST)
[AMBER] how to use GLYCAM04 for carbonhydrate in amber9? sculiujl (Sun Nov 29 2009 - 21:39:08 CST)
[AMBER] reagarding Dihedral PCA jani sahil (Mon Nov 30 2009 - 00:24:28 CST)
[AMBER] regarding Dihedral PCA jani sahil (Mon Nov 30 2009 - 00:25:08 CST)
[AMBER] distance-dependent dielectric constant minimization Rilei Yu (Mon Nov 30 2009 - 01:02:32 CST)
Re: [AMBER] how to use GLYCAM04 for carbonhydrate in amber9? Karl Kirschner (Mon Nov 30 2009 - 02:53:27 CST)
[AMBER] trajout problem Anna Reymer (Mon Nov 30 2009 - 06:03:38 CST)
Re: [AMBER] trajout problem Carlos Simmerling (Mon Nov 30 2009 - 06:09:05 CST)
[AMBER] problem with FAD in tleap M. Shahid (Mon Nov 30 2009 - 06:17:09 CST)
Re: [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov (Mon Nov 30 2009 - 06:56:42 CST)
RE: [AMBER] trajout problem Anna Reymer (Mon Nov 30 2009 - 06:58:39 CST)
Re: [AMBER] distance-dependent dielectric constant minimization case (Mon Nov 30 2009 - 07:02:11 CST)
Re: [AMBER] problem with FAD in tleap FyD (Mon Nov 30 2009 - 07:02:59 CST)
Re: [AMBER] problem with FAD in tleap case (Mon Nov 30 2009 - 07:26:37 CST)
Re: [AMBER] heme (united-atom) case (Mon Nov 30 2009 - 07:28:05 CST)
Re: [AMBER] trajout problem Carlos Simmerling (Mon Nov 30 2009 - 07:56:43 CST)
RE: [AMBER] trouble with antechamber Jennifer L. Muzyka (Mon Nov 30 2009 - 08:39:15 CST)
Re: [AMBER] trouble with antechamber case (Mon Nov 30 2009 - 08:57:26 CST)
Re: [AMBER] problem with FAD in tleap M. Shahid (Mon Nov 30 2009 - 09:54:26 CST)
Re: [AMBER] problem with FAD in tleap case (Mon Nov 30 2009 - 11:15:19 CST)
Re: [AMBER] problem with FAD in tleap M. Shahid (Mon Nov 30 2009 - 12:33:35 CST)
[AMBER] Output Does Not Match in Tutorial B1 Wallace Kunin (Mon Nov 30 2009 - 12:38:07 CST)
Re: [AMBER] Output Does Not Match in Tutorial B1 case (Mon Nov 30 2009 - 13:01:20 CST)
Re: [AMBER] trajout problem Sally Pias (Mon Nov 30 2009 - 13:01:52 CST)
Re: [AMBER] Output Does Not Match in Tutorial B1 Bill Ross (Mon Nov 30 2009 - 13:03:19 CST)
Re: [AMBER] Output Does Not Match in Tutorial B1 Wallace Kunin (Mon Nov 30 2009 - 13:11:02 CST)
Re: [AMBER] problem with FAD in tleap FyD (Mon Nov 30 2009 - 13:15:56 CST)
Re: [AMBER] problem with FAD in tleap FyD (Mon Nov 30 2009 - 13:25:15 CST)
Re: [AMBER] Output Does Not Match in Tutorial B1 case (Mon Nov 30 2009 - 13:50:34 CST)
[AMBER] fillratio Qinghua Liao (Mon Nov 30 2009 - 20:38:34 CST)
Re: [AMBER] fillratio Ray Luo (Mon Nov 30 2009 - 21:30:50 CST)
Re: [AMBER] distance-dependent dielectric constant minimization Rilei Yu (Mon Nov 30 2009 - 23:31:58 CST)
Re: [AMBER] Regarding rigid bond aneesh cna (Mon Nov 30 2009 - 23:35:03 CST)
Re: [AMBER] fillratio Qinghua Liao (Mon Nov 30 2009 - 23:59:05 CST)

Last message date: Thu Dec 31 2009 - 22:57:46 CST
Archived on: Thu Dec 31 2009 - 22:58:33 CST

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