Amber Archive Aug 2017 by thread
390 messages
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Starting
Tue Aug 01 2017 - 04:00:02 PDT,
Ending
Thu Aug 31 2017 - 14:00:03 PDT
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[AMBER] If I use source leaprc.gaff command for DNA and protein is it load gaff forcefield or ff14SB force field??
Saikat Pal
(Tue Aug 01 2017 - 03:54:10 PDT)
Re: [AMBER] If I use source leaprc.gaff command for DNA and protein is it load gaff forcefield or ff14SB force field??
Daniel Roe
(Tue Aug 01 2017 - 05:13:12 PDT)
Re: [AMBER] If I use source leaprc.gaff command for DNA and protein is it load gaff forcefield or ff14SB force field??
David A Case
(Tue Aug 01 2017 - 05:21:25 PDT)
[AMBER] Tleap parametrisation of NA+ bound proteins
James Starlight
(Tue Aug 01 2017 - 06:56:25 PDT)
Re: [AMBER] Tleap parametrisation of NA+ bound proteins
David A Case
(Tue Aug 01 2017 - 10:23:42 PDT)
Re: [AMBER] Tleap parametrisation of NA+ bound proteins
James Starlight
(Wed Aug 02 2017 - 03:47:22 PDT)
Re: [AMBER] Tleap parametrisation of NA+ bound proteins
James Starlight
(Wed Aug 02 2017 - 06:29:45 PDT)
Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files
Alonso Martinez, Diego
(Tue Aug 01 2017 - 07:48:34 PDT)
Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files
Carlos Simmerling
(Tue Aug 01 2017 - 07:54:17 PDT)
Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files
Alonso Martinez, Diego
(Tue Aug 01 2017 - 09:49:42 PDT)
Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files
Szymon Żaczek
(Tue Aug 01 2017 - 11:17:17 PDT)
Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files
Bill Ross
(Tue Aug 01 2017 - 11:23:02 PDT)
[AMBER] string methods in AMBER16
Chunli Yan
(Tue Aug 01 2017 - 12:00:33 PDT)
Re: [AMBER] string methods in AMBER16
Scott Brozell
(Tue Aug 01 2017 - 12:59:07 PDT)
Re: [AMBER] string methods in AMBER16
Feng Pan
(Tue Aug 01 2017 - 12:59:28 PDT)
Re: [AMBER] string methods in AMBER16
Chunli Yan
(Tue Aug 01 2017 - 13:07:35 PDT)
Re: [AMBER] string methods in AMBER16
Feng Pan
(Tue Aug 01 2017 - 13:37:33 PDT)
Re: [AMBER] string methods in AMBER16
Chunli Yan
(Tue Aug 01 2017 - 13:58:10 PDT)
Re: [AMBER] string methods in AMBER16
Chunli Yan
(Tue Aug 01 2017 - 17:32:58 PDT)
[AMBER] GaMD
Neha Gandhi
(Tue Aug 01 2017 - 16:00:55 PDT)
[AMBER] External force apply along a particular direction
Sanjib Paul
(Wed Aug 02 2017 - 00:21:30 PDT)
Re: [AMBER] Manual parameterization of the TIP4P/2005 water model
Hannes Konegger
(Wed Aug 02 2017 - 01:27:32 PDT)
[AMBER] Tleap processing of membrane protein in amber-16
James Starlight
(Wed Aug 02 2017 - 03:52:14 PDT)
Re: [AMBER] Tleap processing of membrane protein in amber-16
David A Case
(Wed Aug 02 2017 - 06:42:27 PDT)
Re: [AMBER] Tleap processing of membrane protein in amber-16
James Starlight
(Wed Aug 02 2017 - 06:56:45 PDT)
[AMBER] Building of beta strand
Rajarshi Roy
(Wed Aug 02 2017 - 07:51:19 PDT)
Re: [AMBER] Building of beta strand
Hai Nguyen
(Wed Aug 02 2017 - 09:27:47 PDT)
Re: [AMBER] Building of beta strand
Rajarshi Roy
(Wed Aug 02 2017 - 09:32:52 PDT)
Re: [AMBER] Building of beta strand
Hai Nguyen
(Wed Aug 02 2017 - 10:24:54 PDT)
Re: [AMBER] Building of beta strand
Rajarshi Roy
(Wed Aug 02 2017 - 21:34:08 PDT)
Re: [AMBER] Building of beta strand
Daniel Roe
(Mon Aug 07 2017 - 07:28:37 PDT)
Re: [AMBER] Building of beta strand
Hai Nguyen
(Mon Aug 07 2017 - 12:23:58 PDT)
Re: [AMBER] Building of beta strand
Rajarshi Roy
(Tue Aug 08 2017 - 03:40:34 PDT)
[AMBER] Barostat options for membrane protein simulations in NPT
James Starlight
(Wed Aug 02 2017 - 08:21:15 PDT)
[AMBER] A bug with unperturbed charge during tleap processing
James Starlight
(Wed Aug 02 2017 - 11:16:02 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
Bill Ross
(Wed Aug 02 2017 - 21:31:28 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
James Starlight
(Thu Aug 03 2017 - 01:27:19 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
David A Case
(Thu Aug 03 2017 - 04:55:44 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
James Starlight
(Thu Aug 03 2017 - 06:38:34 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
David A Case
(Thu Aug 03 2017 - 18:07:42 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
James Starlight
(Fri Aug 04 2017 - 00:19:27 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
James Starlight
(Fri Aug 04 2017 - 05:34:02 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
James Starlight
(Fri Aug 04 2017 - 11:50:25 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
Bill Ross
(Fri Aug 04 2017 - 12:00:01 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
James Starlight
(Mon Aug 07 2017 - 08:00:19 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
Daniel Roe
(Mon Aug 07 2017 - 09:13:32 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
James Starlight
(Mon Aug 07 2017 - 09:28:15 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
Daniel Roe
(Mon Aug 07 2017 - 09:29:37 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
James Starlight
(Mon Aug 07 2017 - 11:07:31 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
James Starlight
(Wed Aug 09 2017 - 02:21:12 PDT)
Re: [AMBER] A bug with unperturbed charge during tleap processing
Bill Ross
(Wed Aug 09 2017 - 04:03:29 PDT)
[AMBER] pbc box information missing
Albert
(Wed Aug 02 2017 - 13:13:44 PDT)
Re: [AMBER] pbc box information missing
David A Case
(Thu Aug 03 2017 - 04:59:00 PDT)
[AMBER] -rem flags in string method with swarms of trajectories amber
Chunli Yan
(Wed Aug 02 2017 - 14:49:22 PDT)
Re: [AMBER] -rem flags in string method with swarms of trajectories amber
Feng Pan
(Wed Aug 02 2017 - 15:18:46 PDT)
Re: [AMBER] -rem flags in string method with swarms of trajectories amber
Feng Pan
(Wed Aug 02 2017 - 15:24:59 PDT)
Re: [AMBER] -rem flags in string method with swarms of trajectories amber
Chunli Yan
(Wed Aug 02 2017 - 19:02:31 PDT)
[AMBER] amber install
Mohammad Zahidul Hossain Khan
(Wed Aug 02 2017 - 15:04:19 PDT)
Re: [AMBER] amber install
David A Case
(Thu Aug 03 2017 - 05:02:01 PDT)
[AMBER] amber install
Mohammad Zahidul Hossain Khan
(Wed Aug 02 2017 - 19:06:31 PDT)
Re: [AMBER] amber install
liu junjun
(Wed Aug 02 2017 - 20:00:36 PDT)
Re: [AMBER] amber install
Hai Nguyen
(Wed Aug 02 2017 - 21:34:18 PDT)
[AMBER] different crd format?
Albert
(Thu Aug 03 2017 - 00:46:25 PDT)
Re: [AMBER] different crd format?
David A Case
(Thu Aug 03 2017 - 05:06:31 PDT)
Re: [AMBER] different crd format?
Daniel Roe
(Mon Aug 07 2017 - 07:25:42 PDT)
[AMBER] amber frcmod file
Neha Gandhi
(Thu Aug 03 2017 - 01:51:40 PDT)
[AMBER] Number of triangulated 3-point waters found: 0
Shilpa Gupta
(Thu Aug 03 2017 - 03:50:59 PDT)
Re: [AMBER] Number of triangulated 3-point waters found: 0
David A Case
(Thu Aug 03 2017 - 05:09:32 PDT)
[AMBER] Applying external force along a particular direction
Sanjib Paul
(Thu Aug 03 2017 - 05:45:29 PDT)
[AMBER] Compilation of Amber 14
Milo Westler
(Thu Aug 03 2017 - 13:01:10 PDT)
Re: [AMBER] Compilation of Amber 14
David A Case
(Thu Aug 03 2017 - 18:20:59 PDT)
Re: [AMBER] Compilation of Amber 14
Milo Westler
(Fri Aug 04 2017 - 09:00:39 PDT)
Re: [AMBER] Compilation of Amber 14
Daniel Roe
(Fri Aug 04 2017 - 11:24:34 PDT)
Re: [AMBER] Compilation of Amber 14
Milo Westler
(Fri Aug 04 2017 - 12:44:56 PDT)
[AMBER] Using polarizable force field ff02 in AMBER 14
Aishwarya Venkatramani
(Thu Aug 03 2017 - 17:00:00 PDT)
[AMBER] Using polarizable force field ff02 in AMBER 14
Aishwarya Venkatramani
(Thu Aug 03 2017 - 20:15:17 PDT)
Re: [AMBER] Using polarizable force field ff02 in AMBER 14
Carlos Simmerling
(Fri Aug 04 2017 - 05:40:05 PDT)
Re: [AMBER] Using polarizable force field ff02 in AMBER 14
Aishwarya Venkatramani
(Fri Aug 04 2017 - 05:47:34 PDT)
Re: [AMBER] Using polarizable force field ff02 in AMBER 14
David A Case
(Fri Aug 04 2017 - 08:18:42 PDT)
Re: [AMBER] Using polarizable force field ff02 in AMBER 14
Aishwarya Venkatramani
(Mon Aug 07 2017 - 11:41:23 PDT)
Re: [AMBER] Using polarizable force field ff02 in AMBER 14
Anthony Cruz-Balberdy
(Mon Aug 07 2017 - 12:41:04 PDT)
Re: [AMBER] Using polarizable force field ff02 in AMBER 14
David A Case
(Mon Aug 07 2017 - 12:54:42 PDT)
[AMBER] RDF for dendrimer
Christopher Gorman
(Fri Aug 04 2017 - 14:18:33 PDT)
Re: [AMBER] RDF for dendrimer
Hai Nguyen
(Fri Aug 04 2017 - 14:34:55 PDT)
Re: [AMBER] RDF for dendrimer
Daniel Roe
(Mon Aug 07 2017 - 08:56:16 PDT)
[AMBER] parametrization of an RNA base
giulia palermo
(Fri Aug 04 2017 - 14:48:01 PDT)
Re: [AMBER] parametrization of an RNA base
Bill Ross
(Fri Aug 04 2017 - 15:29:03 PDT)
Re: [AMBER] parametrization of an RNA base
Andrew Schaub
(Sat Aug 05 2017 - 00:47:50 PDT)
Re: [AMBER] parametrization of an RNA base
David A Case
(Sun Aug 06 2017 - 11:33:40 PDT)
[AMBER] QM/MM calculation in Amber
Albert
(Fri Aug 04 2017 - 23:39:52 PDT)
Re: [AMBER] QM/MM calculation in Amber
David A Case
(Sun Aug 06 2017 - 11:37:38 PDT)
[AMBER] Parameters for HEME-CYS covalent bond
Avijit Rakshit
(Sat Aug 05 2017 - 00:29:21 PDT)
Re: [AMBER] Parameters for HEME-CYS covalent bond
Andrew Schaub
(Sat Aug 05 2017 - 00:43:18 PDT)
Re: [AMBER] Parameters for HEME-CYS covalent bond
Avijit Rakshit
(Sat Aug 05 2017 - 00:56:42 PDT)
Re: [AMBER] Parameters for HEME-CYS covalent bond
Thomas Charles Pochapsky
(Sat Aug 05 2017 - 05:25:31 PDT)
Re: [AMBER] Parameters for HEME-CYS covalent bond
Pengfei Li
(Sat Aug 05 2017 - 20:16:24 PDT)
[AMBER] Amber Atom Types for Non-standard Residue
david kastner
(Sat Aug 05 2017 - 18:08:23 PDT)
[AMBER] How best to build a solvent box for a solute with changing dimensions?
Kasprzak, Wojciech (NIH/NCI) [C]
(Mon Aug 07 2017 - 08:53:57 PDT)
Re: [AMBER] How best to build a solvent box for a solute with changing dimensions?
Daniel Roe
(Mon Aug 07 2017 - 09:26:13 PDT)
[AMBER] gaff2 atom type (cs) is not in PARMCHK.DAT
Tsai Kun-Lin
(Mon Aug 07 2017 - 17:51:44 PDT)
Re: [AMBER] gaff2 atom type (cs) is not in PARMCHK.DAT
Scott Brozell
(Tue Aug 08 2017 - 14:22:54 PDT)
Re: [AMBER] gaff2 atom type (cs) is not in PARMCHK.DAT
Scott Brozell
(Tue Aug 08 2017 - 20:06:29 PDT)
Re: [AMBER] gaff2 atom type (cs) is not in PARMCHK.DAT
David A Case
(Wed Aug 09 2017 - 04:42:57 PDT)
Re: [AMBER] gaff2 atom type (cs) is not in PARMCHK.DAT
Junmei Wang
(Tue Aug 15 2017 - 04:51:09 PDT)
[AMBER] results for string methods
Chunli Yan
(Mon Aug 07 2017 - 18:49:45 PDT)
Re: [AMBER] results for string methods
Feng Pan
(Tue Aug 08 2017 - 10:27:38 PDT)
Re: [AMBER] results for string methods
Chunli Yan
(Tue Aug 08 2017 - 10:33:36 PDT)
[AMBER] About common Gromacs and Amber Benchmarks
Vlad
(Tue Aug 08 2017 - 00:38:55 PDT)
Re: [AMBER] About common Gromacs and Amber Benchmarks
Hannes Loeffler
(Tue Aug 08 2017 - 00:45:01 PDT)
[AMBER] polarization force field
sangita kachhap
(Tue Aug 08 2017 - 03:25:12 PDT)
Re: [AMBER] polarization force field
David A Case
(Tue Aug 08 2017 - 04:19:40 PDT)
Re: [AMBER] polarization force field
sangita kachhap
(Tue Aug 08 2017 - 05:50:46 PDT)
[AMBER] Problem with leaprc.ff14SB
George Tzotzos
(Tue Aug 08 2017 - 10:50:59 PDT)
Re: [AMBER] Problem with leaprc.ff14SB
David A Case
(Tue Aug 08 2017 - 12:55:00 PDT)
Re: [AMBER] Problem with leaprc.ff14SB
George Tzotzos
(Wed Aug 09 2017 - 08:20:53 PDT)
[AMBER] Error in hbond lifetime analysis
Baig abdullah Al muhit
(Tue Aug 08 2017 - 13:17:41 PDT)
Re: [AMBER] Error in hbond lifetime analysis
Daniel Roe
(Thu Aug 10 2017 - 12:29:17 PDT)
[AMBER] adQMMM overheating
Artur Przydacz
(Tue Aug 08 2017 - 14:03:40 PDT)
Re: [AMBER] adQMMM overheating
Goetz, Andreas
(Tue Aug 08 2017 - 14:58:20 PDT)
Re: [AMBER] adQMMM overheating
Artur Przydacz
(Wed Aug 09 2017 - 05:28:39 PDT)
Re: [AMBER] adQMMM overheating
Goetz, Andreas
(Thu Aug 10 2017 - 00:41:04 PDT)
[AMBER] iat >= 3 in PMEMD and PMEMD.cuda
kurisaki
(Tue Aug 08 2017 - 18:09:51 PDT)
[AMBER] Error in leap on using divalent ion
Chayya Bhargac
(Wed Aug 09 2017 - 06:23:42 PDT)
Re: [AMBER] Error in leap on using divalent ion
David A Case
(Wed Aug 09 2017 - 08:35:44 PDT)
[AMBER] Use of param.Frosst parameters to prepare a ligand in Ambertools?
Anne Nierobisch
(Wed Aug 09 2017 - 06:57:57 PDT)
Re: [AMBER] Use of param.Frosst parameters to prepare a ligand in Ambertools?
David A Case
(Thu Aug 10 2017 - 10:47:54 PDT)
[AMBER] ... RESTARTED DUE TO LINMIN FAILURE ...
Malay Raul
(Wed Aug 09 2017 - 08:23:31 PDT)
Re: [AMBER] ... RESTARTED DUE TO LINMIN FAILURE ...
Jason Swails
(Mon Aug 28 2017 - 19:02:11 PDT)
[AMBER] problems with the HAP tutorial
Kris Feher
(Thu Aug 10 2017 - 03:25:06 PDT)
[AMBER] Query about SPC and SPCE water model
Saikat Pal
(Thu Aug 10 2017 - 04:03:35 PDT)
Re: [AMBER] Query about SPC and SPCE water model
David A Case
(Thu Aug 10 2017 - 04:18:12 PDT)
[AMBER] Is this necessary HOH=SPC command
Saikat Pal
(Thu Aug 10 2017 - 05:32:52 PDT)
Re: [AMBER] Is this necessary HOH=SPC command
David A Case
(Thu Aug 10 2017 - 10:24:21 PDT)
[AMBER] QMMM error: "| Flags: getting box info from netcdf restart file"
Charles Mariasoosai
(Thu Aug 10 2017 - 09:20:24 PDT)
Re: [AMBER] QMMM error: "| Flags: getting box info from netcdf restart file"
Goetz, Andreas
(Thu Aug 10 2017 - 09:52:58 PDT)
[AMBER] QM/MM calculation Amber16/DFTB
Amani Eshtiwi
(Thu Aug 10 2017 - 17:38:48 PDT)
[AMBER] fixing backbone dihedral angles in RNA structure
Asmita Gupta
(Thu Aug 10 2017 - 17:58:58 PDT)
Re: [AMBER] fixing backbone dihedral angles in RNA structure
Bill Ross
(Thu Aug 10 2017 - 18:08:23 PDT)
Re: [AMBER] fixing backbone dihedral angles in RNA structure
Daniel Roe
(Fri Aug 11 2017 - 10:08:09 PDT)
[AMBER] Decomposition Energy Problem with Aspartic Acid only
Jag Silwal
(Fri Aug 11 2017 - 09:18:45 PDT)
[AMBER] Error-Calculating distance between two atoms in CPPTRAJ
Jag Silwal
(Fri Aug 11 2017 - 09:42:21 PDT)
Re: [AMBER] Error-Calculating distance between two atoms in CPPTRAJ
Hai Nguyen
(Fri Aug 11 2017 - 09:52:26 PDT)
Re: [AMBER] Error-Calculating distance between two atoms in CPPTRAJ
Daniel Roe
(Fri Aug 11 2017 - 09:52:39 PDT)
Re: [AMBER] Error-Calculating distance between two atoms in CPPTRAJ
Jag Silwal
(Fri Aug 11 2017 - 10:00:21 PDT)
Re: [AMBER] Error-Calculating distance between two atoms in CPPTRAJ
Daniel Roe
(Fri Aug 11 2017 - 10:03:44 PDT)
[AMBER] The Amber web site is down....
David A Case
(Fri Aug 11 2017 - 09:54:54 PDT)
[AMBER] SASA energy
Mohammad Zahidul Hossain Khan
(Fri Aug 11 2017 - 10:17:57 PDT)
Re: [AMBER] SASA energy
Elvis Martis
(Fri Aug 11 2017 - 12:06:40 PDT)
Re: [AMBER] SASA energy
Mohammad Zahidul Hossain Khan
(Fri Aug 11 2017 - 12:17:08 PDT)
Re: [AMBER] SASA energy
Elvis Martis
(Fri Aug 11 2017 - 20:13:53 PDT)
Re: [AMBER] SASA energy
David A Case
(Sat Aug 12 2017 - 06:32:57 PDT)
Re: [AMBER] SASA energy
Mohammad Zahidul Hossain Khan
(Wed Aug 16 2017 - 11:09:14 PDT)
Re: [AMBER] SASA energy
Daniel Roe
(Wed Aug 16 2017 - 11:39:26 PDT)
Re: [AMBER] SASA energy
Mohammad Zahidul Hossain Khan
(Wed Aug 16 2017 - 11:41:12 PDT)
Re: [AMBER] SASA energy
Daniel Roe
(Wed Aug 16 2017 - 11:51:02 PDT)
[AMBER] Cpptraj to center molecules
Aseel Bala
(Fri Aug 11 2017 - 12:36:06 PDT)
Re: [AMBER] Cpptraj to center molecules
Daniel Roe
(Sat Aug 12 2017 - 10:50:17 PDT)
Re: [AMBER] Cpptraj to center molecules
Aseel Bala Ahmed
(Sat Aug 12 2017 - 12:55:32 PDT)
Re: [AMBER] Cpptraj to center molecules
Bill Ross
(Sat Aug 12 2017 - 13:04:17 PDT)
Re: [AMBER] Cpptraj to center molecules
Bill Ross
(Sat Aug 12 2017 - 13:09:27 PDT)
Re: [AMBER] Cpptraj to center molecules
Aseel Bala Ahmed
(Sat Aug 12 2017 - 13:13:49 PDT)
Re: [AMBER] Cpptraj to center molecules
Bill Ross
(Sat Aug 12 2017 - 13:22:38 PDT)
Re: [AMBER] Cpptraj to center molecules
Aseel Bala Ahmed
(Sat Aug 12 2017 - 14:38:56 PDT)
Re: [AMBER] Cpptraj to center molecules
David A Case
(Sun Aug 13 2017 - 05:32:15 PDT)
Re: [AMBER] Cpptraj to center molecules
Aseel Bala Ahmed
(Sun Aug 13 2017 - 13:27:22 PDT)
[AMBER] Pairwise-Decomposition Energy
Jag Silwal
(Mon Aug 14 2017 - 07:45:08 PDT)
Re: [AMBER] Units in dist_vs_t file from SMD simulation
Xing
(Mon Aug 14 2017 - 21:08:24 PDT)
Re: [AMBER] Units in dist_vs_t file from SMD simulation
Adrian Roitberg
(Tue Aug 15 2017 - 08:22:52 PDT)
Re: [AMBER] Units in dist_vs_t file from SMD simulation
Xing
(Tue Aug 15 2017 - 17:10:51 PDT)
[AMBER] Periodicity of metal bond
Lizelle Lubbe
(Tue Aug 15 2017 - 06:28:22 PDT)
Re: [AMBER] Periodicity of metal bond
Pengfei Li
(Tue Aug 15 2017 - 07:50:00 PDT)
[AMBER] Amber web site is back up
David A Case
(Tue Aug 15 2017 - 06:49:49 PDT)
[AMBER] Amber TI accuracy
Nikolay N. Kuzmich
(Tue Aug 15 2017 - 08:36:59 PDT)
Re: [AMBER] Amber TI accuracy
Adrian Roitberg
(Tue Aug 15 2017 - 08:42:38 PDT)
[AMBER] Pairwise Decomposition-Mask not wroking?
Jag Silwal
(Tue Aug 15 2017 - 09:09:21 PDT)
[AMBER] Amber Install Failure - update does not work
James Kress
(Tue Aug 15 2017 - 15:47:52 PDT)
Re: [AMBER] Amber Install Failure - update does not work
David A Case
(Tue Aug 15 2017 - 20:41:03 PDT)
Re: [AMBER] Amber Install Failure - update does not work
David A Case
(Wed Aug 16 2017 - 07:06:32 PDT)
Re: [AMBER] Amber Install Failure - update does not work
James Kress
(Wed Aug 16 2017 - 08:45:27 PDT)
Re: [AMBER] Amber Install Failure - update does not work
Leandro Bortot
(Thu Aug 17 2017 - 06:21:43 PDT)
[AMBER] How to cross-corrlation matrix betwern 3 Calpha atom
Arpita Goswami
(Tue Aug 15 2017 - 22:34:37 PDT)
[AMBER] Error in Amber16 documentation
Paul Westphälinger
(Wed Aug 16 2017 - 03:30:01 PDT)
Re: [AMBER] Error in Amber16 documentation
Paul Westphälinger
(Wed Aug 16 2017 - 07:32:18 PDT)
[AMBER] grid command in cpptraj
沖本 憲明
(Wed Aug 16 2017 - 07:23:10 PDT)
Re: [AMBER] grid command in cpptraj
Daniel Roe
(Wed Aug 16 2017 - 07:56:10 PDT)
[AMBER] charmmlipid2amber.py with Charm-gui lipids
James Starlight
(Wed Aug 16 2017 - 08:54:01 PDT)
Re: [AMBER] charmmlipid2amber.py with Charm-gui lipids
ABEL Stephane
(Wed Aug 16 2017 - 09:18:54 PDT)
Re: [AMBER] charmmlipid2amber.py with Charm-gui lipids
James Starlight
(Wed Aug 16 2017 - 10:57:40 PDT)
Re: [AMBER] charmmlipid2amber.py with Charm-gui lipids
ABEL Stephane
(Wed Aug 16 2017 - 11:07:34 PDT)
Re: [AMBER] charmmlipid2amber.py with Charm-gui lipids
James Starlight
(Thu Aug 17 2017 - 01:44:42 PDT)
Re: [AMBER] charmmlipid2amber.py with Charm-gui lipids
ABEL Stephane
(Thu Aug 17 2017 - 04:16:30 PDT)
Re: [AMBER] charmmlipid2amber.py with Charm-gui lipids
James Starlight
(Thu Aug 17 2017 - 04:25:35 PDT)
[AMBER] Can pmemd.cuda.MPI do SMD on GPUs?
Xing
(Wed Aug 16 2017 - 14:16:47 PDT)
Re: [AMBER] Can pmemd.cuda.MPI do SMD on GPUs?
Adrian Roitberg
(Wed Aug 16 2017 - 14:55:10 PDT)
Re: [AMBER] Can pmemd.cuda.MPI do SMD on GPUs?
Xing
(Thu Aug 17 2017 - 13:59:12 PDT)
[AMBER] calculate PMF in string methods
Chunli Yan
(Wed Aug 16 2017 - 16:42:03 PDT)
Re: [AMBER] calculate PMF in string methods
Feng Pan
(Thu Aug 17 2017 - 15:48:55 PDT)
Re: [AMBER] calculate PMF in string methods
Chunli Yan
(Thu Aug 17 2017 - 19:22:45 PDT)
Re: [AMBER] calculate PMF in string methods
Chunli Yan
(Thu Aug 17 2017 - 19:25:57 PDT)
Re: [AMBER] calculate PMF in string methods
Carlos Simmerling
(Fri Aug 18 2017 - 12:40:19 PDT)
Re: [AMBER] calculate PMF in string methods
Chunli Yan
(Fri Aug 18 2017 - 14:43:41 PDT)
Re: [AMBER] calculate PMF in string methods
Feng Pan
(Sat Aug 19 2017 - 00:28:35 PDT)
[AMBER] how to implement GEN keyword in QM/MM with external program
chemist zobia
(Wed Aug 16 2017 - 22:31:16 PDT)
Re: [AMBER] how to implement GEN keyword in QM/MM with external program
Goetz, Andreas
(Fri Aug 18 2017 - 11:33:04 PDT)
[AMBER] Install in gpu AMBER14 for high performance computer
Saikat Pal
(Thu Aug 17 2017 - 08:46:02 PDT)
Re: [AMBER] Install in gpu AMBER14 for high performance computer
David A Case
(Thu Aug 17 2017 - 11:57:18 PDT)
Re: [AMBER] Install in gpu AMBER14 for high performance computer
Saikat Pal
(Thu Aug 17 2017 - 23:57:46 PDT)
[AMBER] Thermodynamic Integration using PMEMD
Roma Mukhopadhyay
(Thu Aug 17 2017 - 11:24:00 PDT)
Re: [AMBER] Thermodynamic Integration using PMEMD
Hannes Loeffler
(Fri Aug 18 2017 - 00:09:45 PDT)
Re: [AMBER] Thermodynamic Integration using PMEMD
Roma Mukhopadhyay
(Fri Aug 18 2017 - 06:34:32 PDT)
Re: [AMBER] Thermodynamic Integration using PMEMD
Hannes Loeffler
(Fri Aug 18 2017 - 07:20:10 PDT)
Re: [AMBER] Thermodynamic Integration using PMEMD
Roma Mukhopadhyay
(Fri Aug 18 2017 - 09:13:46 PDT)
Re: [AMBER] Thermodynamic Integration using PMEMD
Hannes Loeffler
(Fri Aug 18 2017 - 09:36:24 PDT)
[AMBER] Amber16/DFTB and bromine
Amani Eshtiwi
(Thu Aug 17 2017 - 12:32:01 PDT)
Re: [AMBER] Amber16/DFTB and bromine
Goetz, Andreas
(Thu Aug 17 2017 - 12:53:05 PDT)
Re: [AMBER] Amber16/DFTB and bromine
Amani Eshtiwi
(Thu Aug 17 2017 - 13:20:17 PDT)
Re: [AMBER] Amber16/DFTB and bromine
Goetz, Andreas
(Fri Aug 18 2017 - 12:19:55 PDT)
Re: [AMBER] Amber16/DFTB and bromine
Gustavo Seabra
(Fri Aug 18 2017 - 13:02:26 PDT)
Re: [AMBER] Amber16/DFTB and bromine
Amani Eshtiwi
(Fri Aug 18 2017 - 15:37:35 PDT)
Re: [AMBER] Amber16/DFTB and bromine
Amani Eshtiwi
(Fri Aug 18 2017 - 15:46:46 PDT)
Re: [AMBER] Amber16/DFTB and bromine
Amani Eshtiwi
(Fri Aug 18 2017 - 16:26:55 PDT)
Re: [AMBER] Amber16/DFTB and bromine
Amani Eshtiwi
(Fri Aug 18 2017 - 16:44:18 PDT)
Re: [AMBER] Amber16/DFTB and bromine
Gustavo Seabra
(Fri Aug 18 2017 - 18:51:19 PDT)
Re: [AMBER] Amber16/DFTB and bromine
Amani Eshtiwi
(Fri Aug 18 2017 - 19:04:12 PDT)
Re: [AMBER] Amber16/DFTB and bromine
Gustavo Seabra
(Fri Aug 18 2017 - 19:06:32 PDT)
Re: [AMBER] Amber16/DFTB and bromine
Amani Eshtiwi
(Fri Aug 18 2017 - 19:11:18 PDT)
Re: [AMBER] Amber16/DFTB and bromine
Amani Eshtiwi
(Fri Aug 18 2017 - 19:32:43 PDT)
[AMBER] An equilibration of the membrane protein prepared by charmm-gui
James Starlight
(Fri Aug 18 2017 - 00:23:24 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
ABEL Stephane
(Fri Aug 18 2017 - 03:30:45 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
James Starlight
(Fri Aug 18 2017 - 06:36:28 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
ABEL Stephane
(Fri Aug 18 2017 - 07:28:23 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
James Starlight
(Fri Aug 18 2017 - 07:33:21 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
ABEL Stephane
(Fri Aug 18 2017 - 07:51:13 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
James Starlight
(Tue Aug 22 2017 - 07:26:11 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
James Starlight
(Wed Aug 23 2017 - 08:50:58 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
James Starlight
(Fri Aug 25 2017 - 14:26:46 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
James Starlight
(Thu Aug 31 2017 - 07:52:04 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
Amy Rice
(Thu Aug 31 2017 - 08:23:31 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
James Starlight
(Thu Aug 31 2017 - 09:31:12 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
James Starlight
(Thu Aug 31 2017 - 09:57:38 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
James Kress
(Thu Aug 31 2017 - 13:28:38 PDT)
[AMBER] How many GPU card is working
Saikat Pal
(Fri Aug 18 2017 - 04:33:47 PDT)
Re: [AMBER] How many GPU card is working
Daniel Roe
(Fri Aug 18 2017 - 05:15:09 PDT)
Re: [AMBER] How many GPU card is working
Saikat Pal
(Fri Aug 18 2017 - 05:35:48 PDT)
Re: [AMBER] How many GPU card is working
Daniel Roe
(Fri Aug 18 2017 - 06:09:12 PDT)
Re: [AMBER] How many GPU card is working
Saikat Pal
(Fri Aug 18 2017 - 06:50:13 PDT)
Re: [AMBER] How many GPU card is working
Daniel Roe
(Fri Aug 18 2017 - 07:13:37 PDT)
Re: [AMBER] How many GPU card is working
Saikat Pal
(Fri Aug 18 2017 - 07:33:34 PDT)
[AMBER] A restrain mask for membrane protein simulation
James Starlight
(Fri Aug 18 2017 - 07:17:05 PDT)
Re: [AMBER] A restrain mask for membrane protein simulation
ABEL Stephane
(Fri Aug 18 2017 - 07:31:24 PDT)
Re: [AMBER] A restrain mask for membrane protein simulation
James Starlight
(Fri Aug 18 2017 - 07:34:41 PDT)
[AMBER] Problem with tleap (non atom type)
Parviz Seifpanahi Shabane
(Fri Aug 18 2017 - 07:51:06 PDT)
Re: [AMBER] Problem with tleap (non atom type)
Bill Ross
(Fri Aug 18 2017 - 10:20:39 PDT)
Re: [AMBER] Problem with tleap (non atom type)
David A Case
(Fri Aug 18 2017 - 13:44:33 PDT)
Re: [AMBER] Problem with tleap (non atom type)
Bill Ross
(Fri Aug 18 2017 - 13:48:09 PDT)
[AMBER] Deprotonation of Tyr
Sowmya Indrakumar
(Fri Aug 18 2017 - 08:24:46 PDT)
Re: [AMBER] Deprotonation of Tyr
Adrian Roitberg
(Fri Aug 18 2017 - 08:38:10 PDT)
Re: [AMBER] Deprotonation of Tyr
Sowmya Indrakumar
(Fri Aug 18 2017 - 08:57:44 PDT)
Re: [AMBER] Deprotonation of Tyr
Sowmya Indrakumar
(Sun Aug 20 2017 - 06:45:32 PDT)
Re: [AMBER] Deprotonation of Tyr
pancham lal Gupta
(Wed Aug 30 2017 - 08:40:08 PDT)
[AMBER] Impose bond lengths
RYDER WHITTAKER HAWKINS
(Fri Aug 18 2017 - 08:35:58 PDT)
Re: [AMBER] Impose bond lengths
Bill Ross
(Fri Aug 18 2017 - 10:18:30 PDT)
[AMBER] Performed MMPBSA.py.MPI failed in Amber16 with Ambertools 17
JiYuan Liu
(Fri Aug 18 2017 - 10:28:05 PDT)
Re: [AMBER] Performed MMPBSA.py.MPI failed in Amber16 with Ambertools 17
David A Case
(Fri Aug 18 2017 - 13:59:41 PDT)
Re: [AMBER] Performed MMPBSA.py.MPI failed in Amber16 with Ambertools 17
Jiyuan Liu
(Sat Aug 19 2017 - 05:48:07 PDT)
Re: [AMBER] Performed MMPBSA.py.MPI failed in Amber16 with Ambertools 17
Jiyuan Liu
(Sun Aug 20 2017 - 07:35:09 PDT)
Re: [AMBER] Performed MMPBSA.py.MPI failed in Amber16 with Ambertools 17
Jiyuan Liu
(Mon Aug 21 2017 - 07:22:48 PDT)
[AMBER] Install amber 14 in nvidia gpu tesla k40
Saikat Pal
(Sat Aug 19 2017 - 00:24:36 PDT)
Re: [AMBER] Install amber 14 in nvidia gpu tesla k40
David A Case
(Sat Aug 19 2017 - 09:04:59 PDT)
[AMBER] Analyzing the aMD results - Tutorial 22
carmine marco morgillo
(Sat Aug 19 2017 - 08:51:37 PDT)
[AMBER] How to move the protein to the corner of the box.
Parviz Seifpanahi Shabane
(Sat Aug 19 2017 - 13:49:37 PDT)
Re: [AMBER] How to move the protein to the corner of the box.
David A Case
(Sun Aug 20 2017 - 06:05:52 PDT)
[AMBER] Calculation the Area per lipids using cpptraj
James Starlight
(Mon Aug 21 2017 - 01:19:35 PDT)
Re: [AMBER] Calculation the Area per lipids using cpptraj
Daniel Roe
(Mon Aug 21 2017 - 06:28:04 PDT)
Re: [AMBER] Calculation the Area per lipids using cpptraj
James Starlight
(Wed Aug 23 2017 - 06:33:35 PDT)
Re: [AMBER] Calculation the Area per lipids using cpptraj
Daniel Roe
(Tue Aug 29 2017 - 12:35:33 PDT)
Re: [AMBER] Calculation the Area per lipids using cpptraj
James Starlight
(Wed Aug 30 2017 - 01:00:03 PDT)
[AMBER] mpirun -np 1 and mpirun -np 2 Peer to Peer support problem
Saikat Pal
(Mon Aug 21 2017 - 03:22:17 PDT)
[AMBER] Deprotonation of Tyr
Sowmya Indrakumar
(Mon Aug 21 2017 - 08:37:54 PDT)
Re: [AMBER] Deprotonation of Tyr
Marcos Serrou do Amaral
(Mon Aug 21 2017 - 12:34:52 PDT)
Re: [AMBER] Deprotonation of Tyr
Sowmya Indrakumar
(Mon Aug 21 2017 - 13:19:15 PDT)
Re: [AMBER] Deprotonation of Tyr
Marcos Serrou do Amaral
(Mon Aug 21 2017 - 16:25:46 PDT)
[AMBER] (kein Betreff)
Traeg, Johannes
(Tue Aug 22 2017 - 01:47:49 PDT)
Re: [AMBER] (kein Betreff)
Hannes Loeffler
(Tue Aug 22 2017 - 01:56:40 PDT)
Re: [AMBER] (kein Betreff)
Traeg, Johannes
(Tue Aug 22 2017 - 03:31:48 PDT)
Re: [AMBER] (kein Betreff)
David A Case
(Tue Aug 22 2017 - 05:14:16 PDT)
Re: [AMBER] (kein Betreff)
Junmei Wang
(Tue Aug 29 2017 - 06:54:03 PDT)
Re: [AMBER] (kein Betreff)
Junmei Wang
(Tue Aug 29 2017 - 07:02:48 PDT)
Re: [AMBER] (kein Betreff)
Traeg, Johannes
(Wed Aug 30 2017 - 02:28:48 PDT)
Re: [AMBER] (kein Betreff)
Junmei Wang
(Wed Aug 30 2017 - 08:27:44 PDT)
Re: [AMBER] (kein Betreff)
Traeg, Johannes
(Thu Aug 31 2017 - 01:11:33 PDT)
Re: [AMBER] Deprotonation of Tyr using Parmed
Sowmya Indrakumar
(Tue Aug 22 2017 - 06:41:11 PDT)
Re: [AMBER] Deprotonation of Tyr using Parmed
Sowmya Indrakumar
(Tue Aug 22 2017 - 07:08:06 PDT)
Re: [AMBER] Deprotonation of Tyr using Parmed
Jason Swails
(Thu Aug 24 2017 - 02:01:16 PDT)
Re: [AMBER] Deprotonation of Tyr using Parmed
Sowmya Indrakumar
(Thu Aug 24 2017 - 06:04:32 PDT)
Re: [AMBER] Deprotonation of Tyr using Parmed
Jason Swails
(Mon Aug 28 2017 - 18:57:59 PDT)
[AMBER] Thermodynamic Integration question
Lin Song
(Tue Aug 22 2017 - 15:51:08 PDT)
Re: [AMBER] Thermodynamic Integration question
David Cerutti
(Tue Aug 22 2017 - 16:01:29 PDT)
Re: [AMBER] Thermodynamic Integration question
Lin Song
(Tue Aug 22 2017 - 16:33:43 PDT)
[AMBER] angle of domain movement calculation
sangita kachhap
(Wed Aug 23 2017 - 03:05:29 PDT)
Re: [AMBER] angle of domain movement calculation
Carlos Simmerling
(Wed Aug 23 2017 - 08:58:53 PDT)
[AMBER] Binding free energy for dimeric form
Maryam Hamzehee
(Wed Aug 23 2017 - 04:55:07 PDT)
[AMBER] Amber workshop?
Georg Kuenze
(Wed Aug 23 2017 - 14:51:23 PDT)
Re: [AMBER] Amber workshop?
Ross Walker
(Thu Aug 24 2017 - 09:54:28 PDT)
[AMBER] Regarding GPU card
MOHD HOMAIDUR RAHMAN
(Thu Aug 24 2017 - 07:32:10 PDT)
Re: [AMBER] Regarding GPU card
Alessandro Contini
(Thu Aug 24 2017 - 07:41:11 PDT)
Re: [AMBER] Regarding GPU card
Ross Walker
(Thu Aug 24 2017 - 09:58:30 PDT)
Re: [AMBER] Regarding GPU card
Scott Le Grand
(Thu Aug 24 2017 - 11:25:17 PDT)
[AMBER] Closest velocities
Pär Håkansson
(Thu Aug 24 2017 - 12:20:04 PDT)
Re: [AMBER] Closest velocities
Daniel Roe
(Thu Aug 24 2017 - 13:00:49 PDT)
Re: [AMBER] Closest velocities
Pär Håkansson
(Tue Aug 29 2017 - 00:31:23 PDT)
Re: [AMBER] Closest velocities
Daniel Roe
(Tue Aug 29 2017 - 12:26:03 PDT)
[AMBER] RMSD colvar
Chunli Yan
(Thu Aug 24 2017 - 12:57:01 PDT)
Re: [AMBER] RMSD colvar
Feng Pan
(Sun Aug 27 2017 - 21:09:03 PDT)
Re: [AMBER] cphstats Error: Could not open or parse cpin file
Vincent Ustach
(Thu Aug 24 2017 - 20:22:28 PDT)
Re: [AMBER] cphstats Error: Could not open or parse cpin file
Jason Swails
(Mon Aug 28 2017 - 18:52:15 PDT)
[AMBER] Discrepancies in MMPBSA calculations for the same trajectory
Andrew.Warden.csiro.au
(Thu Aug 24 2017 - 21:42:06 PDT)
[AMBER] LINMIN Error while minimizing
Chayya Bhargac
(Thu Aug 24 2017 - 23:05:10 PDT)
Re: [AMBER] LINMIN Error while minimizing
Bill Ross
(Thu Aug 24 2017 - 23:10:23 PDT)
Re: [AMBER] LINMIN Error while minimizing
Chayya Bhargac
(Fri Aug 25 2017 - 08:19:38 PDT)
Re: [AMBER] LINMIN Error while minimizing
Bill Ross
(Fri Aug 25 2017 - 09:58:51 PDT)
Re: [AMBER] LINMIN Error while minimizing
James Kress
(Fri Aug 25 2017 - 10:36:32 PDT)
Re: [AMBER] LINMIN Error while minimizing
David A Case
(Fri Aug 25 2017 - 13:07:09 PDT)
[AMBER] RESP calculation in MCPBpy
Lizelle Lubbe
(Fri Aug 25 2017 - 03:39:18 PDT)
[AMBER] TIP3p lennard jones parameters
Lizelle Lubbe
(Fri Aug 25 2017 - 08:19:10 PDT)
Re: [AMBER] TIP3p lennard jones parameters
David A Case
(Fri Aug 25 2017 - 13:17:08 PDT)
Re: [AMBER] TIP3p lennard jones parameters
Lizelle Lubbe
(Thu Aug 31 2017 - 01:45:57 PDT)
[AMBER] Hybridization problem in Amber
Julian Stys
(Fri Aug 25 2017 - 12:14:24 PDT)
Re: [AMBER] Hybridization problem in Amber
David A Case
(Sun Aug 27 2017 - 14:08:55 PDT)
Re: [AMBER] Hybridization problem in Amber
Julian Stys
(Mon Aug 28 2017 - 15:11:08 PDT)
[AMBER] Fw: Ambermd Error: an illegal memory access was encountered launching kernel kClearForces
Silvana Valdebenito Silva
(Sat Aug 26 2017 - 10:13:16 PDT)
Re: [AMBER] Fw: Ambermd Error: an illegal memory access was encountered launching kernel kClearForces
David A Case
(Sun Aug 27 2017 - 13:49:16 PDT)
[AMBER] wrong ligand geometry
Thomas Evangelidis
(Sat Aug 26 2017 - 12:41:33 PDT)
Re: [AMBER] wrong ligand geometry
David A Case
(Sun Aug 27 2017 - 05:40:51 PDT)
[AMBER] Error while running antechamber for modified amino acid residue
Rajarshi Roy
(Sun Aug 27 2017 - 04:50:28 PDT)
Re: [AMBER] Error while running antechamber for modified amino acid residue
David A Case
(Sun Aug 27 2017 - 05:57:40 PDT)
Re: [AMBER] Error while running antechamber for modified amino acid residue
Rajarshi Roy
(Sun Aug 27 2017 - 09:22:33 PDT)
[AMBER] How to put the restrain on just part of the system.
Parviz Seifpanahi Shabane
(Sun Aug 27 2017 - 08:05:24 PDT)
Re: [AMBER] How to put the restrain on just part of the system.
David A Case
(Sun Aug 27 2017 - 13:45:10 PDT)
Re: [AMBER] How to put the restrain on just part of the system.
Parviz Seifpanahi Shabane
(Sun Aug 27 2017 - 15:57:17 PDT)
Re: [AMBER] How to put the restrain on just part of the system.
Daniel Roe
(Mon Aug 28 2017 - 05:42:13 PDT)
Re: [AMBER] How to put the restrain on just part of the system.
James Kress
(Mon Aug 28 2017 - 15:33:13 PDT)
[AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file?
Jewgeni Starikow
(Sun Aug 27 2017 - 14:41:29 PDT)
Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file?
Bill Ross
(Sun Aug 27 2017 - 15:38:45 PDT)
Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file?
Jewgeni Starikow
(Sun Aug 27 2017 - 22:24:26 PDT)
Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file?
Bill Ross
(Sun Aug 27 2017 - 23:16:21 PDT)
Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file?
Jewgeni Starikow
(Mon Aug 28 2017 - 00:26:42 PDT)
Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file?
Bill Ross
(Mon Aug 28 2017 - 01:44:35 PDT)
Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file?
Hai Nguyen
(Sun Aug 27 2017 - 19:01:01 PDT)
Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file?
Jewgeni Starikow
(Sun Aug 27 2017 - 22:22:29 PDT)
Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file?
Daniel Roe
(Mon Aug 28 2017 - 05:39:36 PDT)
Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file?
Jewgeni Starikow
(Mon Aug 28 2017 - 06:45:45 PDT)
[AMBER] Segmentation error in minimization
Lizelle Lubbe
(Mon Aug 28 2017 - 05:49:06 PDT)
Re: [AMBER] Segmentation error in minimization
David A Case
(Mon Aug 28 2017 - 08:03:23 PDT)
[AMBER] Creation of coordinate and topology file for protei-ligand complex
Ashok Kumar
(Mon Aug 28 2017 - 09:03:00 PDT)
Re: [AMBER] Creation of coordinate and topology file for protei-ligand complex
Bill Ross
(Mon Aug 28 2017 - 09:06:28 PDT)
Re: [AMBER] Creation of coordinate and topology file for protei-ligand complex
Bill Ross
(Mon Aug 28 2017 - 09:08:38 PDT)
Re: [AMBER] Creation of coordinate and topology file for protei-ligand complex
David A Case
(Mon Aug 28 2017 - 10:42:34 PDT)
[AMBER] problem in minimization and heating
Saikat Pal
(Tue Aug 29 2017 - 00:42:37 PDT)
Re: [AMBER] problem in minimization and heating
Bill Ross
(Tue Aug 29 2017 - 00:50:46 PDT)
Re: [AMBER] problem in minimization and heating
David A Case
(Tue Aug 29 2017 - 04:53:28 PDT)
[AMBER] Query regarding water-water interaction potential in GIST output
Rakesh Srivastava
(Tue Aug 29 2017 - 04:56:54 PDT)
Re: [AMBER] Query regarding water-water interaction potential in GIST output
Steven Ramsey
(Tue Aug 29 2017 - 07:03:40 PDT)
Re: [AMBER] Query regarding water-water interaction potential in GIST output
Rakesh Srivastava
(Tue Aug 29 2017 - 21:22:07 PDT)
[AMBER] Distance Restraint using COM for Umbrella Sampling
Suchetana Gupta
(Tue Aug 29 2017 - 05:56:49 PDT)
Re: [AMBER] Distance Restraint using COM for Umbrella Sampling
Daniel Roe
(Tue Aug 29 2017 - 12:29:06 PDT)
[AMBER] For restraint heating
Saikat Pal
(Tue Aug 29 2017 - 07:06:08 PDT)
Re: [AMBER] For restraint heating
Bill Ross
(Tue Aug 29 2017 - 07:13:34 PDT)
Re: [AMBER] For restraint heating
Saikat Pal
(Tue Aug 29 2017 - 07:29:41 PDT)
[AMBER] Clarification about Gnp settings in MM/PBSA
Guqin Shi
(Tue Aug 29 2017 - 11:35:51 PDT)
Re: [AMBER] Clarification about Gnp settings in MM/PBSA
Guqin Shi
(Tue Aug 29 2017 - 13:00:47 PDT)
[AMBER] TIP3PBOX for membrane system
James Starlight
(Wed Aug 30 2017 - 02:25:00 PDT)
Re: [AMBER] TIP3PBOX for membrane system
Bill Ross
(Wed Aug 30 2017 - 02:30:58 PDT)
Re: [AMBER] TIP3PBOX for membrane system
James Starlight
(Wed Aug 30 2017 - 02:39:21 PDT)
Re: [AMBER] TIP3PBOX for membrane system
Bill Ross
(Wed Aug 30 2017 - 02:41:50 PDT)
Re: [AMBER] TIP3PBOX for membrane system
James Starlight
(Wed Aug 30 2017 - 02:42:57 PDT)
Re: [AMBER] TIP3PBOX for membrane system
Bill Ross
(Wed Aug 30 2017 - 02:43:17 PDT)
Re: [AMBER] TIP3PBOX for membrane system
James Starlight
(Wed Aug 30 2017 - 02:54:33 PDT)
[AMBER] Calculate lateral self-diffusion coefficient for POPE embedded protein system
carmine marco morgillo
(Wed Aug 30 2017 - 15:51:20 PDT)
Re: [AMBER] Calculate lateral self-diffusion coefficient for POPE embedded protein system
Daniel Roe
(Thu Aug 31 2017 - 06:03:18 PDT)
[AMBER] convert .mae topology to .prmtop topology?
Marcelo Andrade Chagas
(Wed Aug 30 2017 - 20:14:56 PDT)
Re: [AMBER] convert .mae topology to .prmtop topology?
Daniel Roe
(Thu Aug 31 2017 - 06:15:31 PDT)
[AMBER] frcmod file format
Lizelle Lubbe
(Thu Aug 31 2017 - 03:03:45 PDT)
Re: [AMBER] frcmod file format
Pengfei Li
(Thu Aug 31 2017 - 07:48:34 PDT)
Re: [AMBER] AMBER Digest, Vol 2042, Issue 1
Suchetana Gupta
(Thu Aug 31 2017 - 03:13:38 PDT)
[AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
Parviz Seifpanahi Shabane
(Thu Aug 31 2017 - 08:11:44 PDT)
Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
Bill Ross
(Thu Aug 31 2017 - 10:02:55 PDT)
Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
Parviz Seifpanahi Shabane
(Thu Aug 31 2017 - 10:11:49 PDT)
Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
Bill Ross
(Thu Aug 31 2017 - 12:50:42 PDT)
[AMBER] Webinar: “An AI Quantum Breakthrough: ANAKIN-ME”
Mark Berger
(Thu Aug 31 2017 - 13:33:34 PDT)
Last message date
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Thu Aug 31 2017 - 14:00:03 PDT
Archived on
: Fri Nov 15 2024 - 05:55:37 PST
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