Amber Archive Dec 2018 by thread
309 messages
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Starting
Sun Dec 02 2018 - 07:30:02 PST,
Ending
Mon Dec 31 2018 - 07:30:02 PST
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[AMBER] Extracting PDBs every 'N" ns
Jag Silwal
(Sun Dec 02 2018 - 07:16:15 PST)
[AMBER] Ris: Extracting PDBs every 'N" ns
Casalini Tommaso
(Sun Dec 02 2018 - 07:45:16 PST)
Re: [AMBER] Ris: Extracting PDBs every 'N" ns
Jag Silwal
(Sun Dec 02 2018 - 07:54:44 PST)
[AMBER] Ris: Ris: Extracting PDBs every 'N" ns
Casalini Tommaso
(Sun Dec 02 2018 - 08:02:03 PST)
Re: [AMBER] Extracting PDBs every 'N" ns
David Case
(Sun Dec 02 2018 - 11:40:27 PST)
Re: [AMBER] Extracting PDBs every 'N" ns
Jag Silwal
(Mon Dec 03 2018 - 02:25:11 PST)
Re: [AMBER] Extracting PDBs every 'N" ns
Daniel Roe
(Mon Dec 03 2018 - 11:14:20 PST)
[AMBER] RMSD vs RMSF
Xiaoyu Wang
(Sun Dec 02 2018 - 16:28:45 PST)
Re: [AMBER] RMSD vs RMSF
Elvis Martis
(Sun Dec 02 2018 - 20:51:24 PST)
Re: [AMBER] cpptraj error
Rajbinder Kaur Virk
(Sun Dec 02 2018 - 22:16:28 PST)
Re: [AMBER] cpptraj error
Daniel Roe
(Mon Dec 03 2018 - 11:23:50 PST)
Re: [AMBER] cpptraj error
Rajbinder Kaur Virk
(Tue Dec 04 2018 - 01:18:29 PST)
[AMBER] TUTORIAL
Charu Sharma (JRF)
(Mon Dec 03 2018 - 01:54:35 PST)
Re: [AMBER] TUTORIAL
Bill Ross
(Mon Dec 03 2018 - 02:24:26 PST)
Re: [AMBER] TUTORIAL
Charu Sharma (JRF)
(Mon Dec 03 2018 - 02:34:12 PST)
Re: [AMBER] TUTORIAL
Bill Ross
(Mon Dec 03 2018 - 02:44:42 PST)
Re: [AMBER] TUTORIAL
Charu Sharma (JRF)
(Mon Dec 03 2018 - 02:53:05 PST)
Re: [AMBER] TUTORIAL
Bill Ross
(Mon Dec 03 2018 - 03:05:37 PST)
[AMBER] minimization difficulties
Kimia Sh
(Mon Dec 03 2018 - 02:46:16 PST)
Re: [AMBER] minimization difficulties
Bill Ross
(Mon Dec 03 2018 - 03:10:05 PST)
Re: [AMBER] minimization difficulties
David A Case
(Mon Dec 03 2018 - 07:05:32 PST)
[AMBER] MCPB.py problems For atom (.R<AL1 380>.A<CL2 1>) could not find vdW (or other) parameters for type (Y1)
Jinfeng Chen
(Mon Dec 03 2018 - 03:42:29 PST)
Re: [AMBER] MCPB.py problems For atom (.R<AL1 380>.A<CL2 1>) could not find vdW (or other) parameters for type (Y1)
Pengfei Li
(Sat Dec 08 2018 - 18:34:00 PST)
[AMBER] Delta G pb and Delta G Sa
Keiran Corbett
(Mon Dec 03 2018 - 08:00:11 PST)
Re: [AMBER] Delta G pb and Delta G Sa
Wesley Michael Botello-Smith
(Mon Dec 03 2018 - 10:19:41 PST)
[AMBER] stapled peptide- PDB bond atom problem
Angew Chemie
(Mon Dec 03 2018 - 08:45:08 PST)
Re: [AMBER] stapled peptide- PDB bond atom problem
David A Case
(Mon Dec 03 2018 - 10:17:07 PST)
Re: [AMBER] Obtaining contact maps with cpptraj
Daniel Roe
(Mon Dec 03 2018 - 12:14:13 PST)
Re: [AMBER] Obtaining contact maps with cpptraj
Alex Spasic
(Tue Dec 04 2018 - 12:25:22 PST)
Re: [AMBER] Minimisation and periodic boundaries.
Daniel Roe
(Mon Dec 03 2018 - 12:21:16 PST)
Re: [AMBER] Linear Interaction Energy
Daniel Roe
(Mon Dec 03 2018 - 12:50:03 PST)
[AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF
Eric Lang
(Tue Dec 04 2018 - 03:36:20 PST)
Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF
Antoine MARION
(Tue Dec 04 2018 - 06:22:56 PST)
Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF
Eric Lang
(Tue Dec 04 2018 - 08:10:14 PST)
Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF
Goetz, Andreas
(Tue Dec 04 2018 - 11:48:59 PST)
Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF
Eric Lang
(Wed Dec 05 2018 - 01:55:43 PST)
Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF
Antoine MARION
(Wed Dec 05 2018 - 02:16:12 PST)
Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF
Goetz, Andreas
(Wed Dec 05 2018 - 11:38:02 PST)
[AMBER] Antechamber give a different total charge from net charge that I specified by -nc
Jinfeng Huang
(Tue Dec 04 2018 - 10:42:41 PST)
[AMBER] Cpptraj usage
Chhaya Singh
(Tue Dec 04 2018 - 14:16:01 PST)
Re: [AMBER] Cpptraj usage
Daniel Roe
(Mon Dec 10 2018 - 06:34:28 PST)
[AMBER] Backbone position restraints as a group
lorenaz
(Wed Dec 05 2018 - 00:49:57 PST)
Re: [AMBER] Backbone position restraints as a group
David A Case
(Thu Dec 06 2018 - 06:12:04 PST)
Re: [AMBER] Backbone position restraints as a group
lorenaz
(Thu Dec 06 2018 - 06:33:07 PST)
[AMBER] regarding graph saving in JPEG
Charu Sharma (JRF)
(Wed Dec 05 2018 - 03:41:05 PST)
Re: [AMBER] regarding graph saving in JPEG
David A Case
(Wed Dec 05 2018 - 05:08:50 PST)
[AMBER] water-induced force on substrate along time
Meng Wu
(Wed Dec 05 2018 - 04:27:45 PST)
Re: [AMBER] water-induced force on substrate along time
Meng Wu
(Wed Dec 05 2018 - 17:31:15 PST)
Re: [AMBER] Minimisation and periodic boundaries
Stejskal, Lenka
(Wed Dec 05 2018 - 08:11:44 PST)
Re: [AMBER] Minimisation and periodic boundaries
Daniel Roe
(Mon Dec 10 2018 - 06:37:06 PST)
[AMBER] Include bound ions as part of the receptor molecule in MMPBSA.py
Nanjie Deng
(Wed Dec 05 2018 - 13:27:11 PST)
Re: [AMBER] Include bound ions as part of the receptor molecule in MMPBSA.py
Keiran Corbett
(Thu Dec 06 2018 - 00:11:17 PST)
Re: [AMBER] Include bound ions as part of the receptor molecule in MMPBSA.py
Christina Bergonzo
(Thu Dec 06 2018 - 05:34:21 PST)
Re: [AMBER] Include bound ions as part of the receptor molecule in MMPBSA.py
Nanjie Deng
(Thu Dec 06 2018 - 19:44:42 PST)
[AMBER] Ambiguous interfaces in generic interface
Pedro H. Oliveira
(Wed Dec 05 2018 - 13:36:24 PST)
Re: [AMBER] Ambiguous interfaces in generic interface
David Case
(Wed Dec 05 2018 - 18:14:38 PST)
[AMBER] tleap does not add OXT when I load a crystal structure
Thomas Evangelidis
(Wed Dec 05 2018 - 15:23:47 PST)
Re: [AMBER] tleap does not add OXT when I load a crystal structure
David Cerutti
(Wed Dec 05 2018 - 16:40:21 PST)
Re: [AMBER] tleap does not add OXT when I load a crystal structure
David Case
(Wed Dec 05 2018 - 18:22:26 PST)
Re: [AMBER] tleap does not add OXT when I load a crystal structure
Thomas Evangelidis
(Thu Dec 06 2018 - 02:09:31 PST)
Re: [AMBER] tleap does not add OXT when I load a crystal structure
David A Case
(Thu Dec 06 2018 - 05:57:53 PST)
[AMBER] numpy related problem in amber
Seketoulie Keretsu
(Wed Dec 05 2018 - 20:05:22 PST)
Re: [AMBER] numpy related problem in amber
Elvis Martis
(Wed Dec 05 2018 - 20:52:32 PST)
Re: [AMBER] numpy related problem in amber
David A Case
(Thu Dec 06 2018 - 06:01:57 PST)
Re: [AMBER] numpy related problem in amber
Seketoulie Keretsu
(Thu Dec 06 2018 - 22:02:39 PST)
Re: [AMBER] numpy related problem in amber
Hai Nguyen
(Thu Dec 06 2018 - 23:30:28 PST)
Re: [AMBER] numpy related problem in amber
Seketoulie Keretsu
(Fri Dec 07 2018 - 03:05:46 PST)
[AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+
Kasprzak, Wojciech (NIH/NCI) [C]
(Thu Dec 06 2018 - 12:21:19 PST)
Re: [AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+
David Cerutti
(Thu Dec 06 2018 - 12:32:55 PST)
Re: [AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+, but no MG
Kasprzak, Wojciech (NIH/NCI) [C]
(Thu Dec 06 2018 - 13:56:21 PST)
Re: [AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+, but no MG
David Case
(Thu Dec 06 2018 - 19:02:59 PST)
Re: [AMBER] Strange TIP3P solvent box - reference to the tutorial
Kasprzak, Wojciech (NIH/NCI) [C]
(Fri Dec 07 2018 - 05:25:54 PST)
[AMBER] Calculate the conduct rate from PMF
Meng Wu
(Thu Dec 06 2018 - 18:51:13 PST)
Re: [AMBER] Calculate the conduct rate from PMF
David A Case
(Mon Dec 10 2018 - 10:41:29 PST)
Re: [AMBER] thermostat on solvent
David Case
(Thu Dec 06 2018 - 19:04:46 PST)
[AMBER] AMBER18 Update Fail (AmberTools Update.10)
Rui Sun
(Fri Dec 07 2018 - 01:31:50 PST)
Re: [AMBER] AMBER18 Update Fail (AmberTools Update.10)
Seketoulie Keretsu
(Fri Dec 07 2018 - 03:04:19 PST)
Re: [AMBER] AMBER18 Update Fail (AmberTools Update.10)
Daniel Roe
(Fri Dec 07 2018 - 05:21:33 PST)
Re: [AMBER] AMBER18 Update Fail (AmberTools Update.10)
Rui Sun
(Fri Dec 07 2018 - 11:28:56 PST)
Re: [AMBER] AMBER18 Update Fail (AmberTools Update.10)
David Case
(Sat Dec 08 2018 - 08:09:00 PST)
[AMBER] vdwmeth
Hosein Geraili Daronkola
(Fri Dec 07 2018 - 06:58:46 PST)
Re: [AMBER] vdwmeth
Hosein Geraili Daronkola
(Fri Dec 07 2018 - 07:55:42 PST)
Re: [AMBER] vdwmeth
Hosein Geraili Daronkola
(Fri Dec 07 2018 - 10:16:49 PST)
Re: [AMBER] vdwmeth
Brian Radak
(Fri Dec 07 2018 - 11:44:59 PST)
Re: [AMBER] vdwmeth
Hosein Geraili Daronkola
(Fri Dec 07 2018 - 14:46:04 PST)
Re: [AMBER] vdwmeth
Brian Radak
(Sat Dec 08 2018 - 07:15:34 PST)
Re: [AMBER] vdwmeth
David Case
(Sat Dec 08 2018 - 08:11:02 PST)
[AMBER] Can a Nudged elastic band (NEB) job run on a single GPU?
Li, Dailin
(Fri Dec 07 2018 - 11:11:49 PST)
Re: [AMBER] Can a Nudged elastic band (NEB) job run on a single GPU?
Ghoreishi, Delaram
(Fri Dec 07 2018 - 11:49:08 PST)
[AMBER] 答复: Can a Nudged elastic band (NEB) job run on a single GPU?
Li, Dailin
(Fri Dec 07 2018 - 12:09:15 PST)
Re: [AMBER] Can a Nudged elastic band (NEB) job run on a single GPU?
Ghoreishi, Delaram
(Fri Dec 07 2018 - 13:10:03 PST)
[AMBER] 答复: Can a Nudged elastic band (NEB) job run on a single GPU?
Li, Dailin
(Fri Dec 07 2018 - 14:16:11 PST)
[AMBER] Dear AMBER members,
대학원/일반대학원 생명과학부
(Sat Dec 08 2018 - 07:46:31 PST)
Re: [AMBER] Dear AMBER members,
David Case
(Sun Dec 09 2018 - 05:39:56 PST)
Re: [AMBER] RESP charge calculation
Pengfei Li
(Sat Dec 08 2018 - 18:27:17 PST)
Re: [AMBER] RESP charge calculation
Aashish Bhatt
(Mon Dec 10 2018 - 02:54:14 PST)
[AMBER] ligand charges for md
Fabian Glaser
(Sun Dec 09 2018 - 08:15:56 PST)
Re: [AMBER] ligand charges for md
David Case
(Sun Dec 09 2018 - 13:08:51 PST)
Re: [AMBER] ligand charges for md
Fabian Glaser
(Tue Dec 11 2018 - 08:33:08 PST)
Re: [AMBER] ligand charges for md
dhaval patel
(Fri Dec 21 2018 - 21:23:04 PST)
[AMBER] Ptraj Command not found.
Pavithra Support
(Sun Dec 09 2018 - 18:37:37 PST)
Re: [AMBER] Ptraj Command not found.
Pratul Agarwal
(Sun Dec 09 2018 - 18:59:43 PST)
Re: [AMBER] Ptraj Command not found.
Daniel Roe
(Mon Dec 10 2018 - 06:04:30 PST)
[AMBER] Problems with installation on Mac with Mojave. (cpptraj??)
Margarita I. Bernal-Uruchurtu
(Mon Dec 10 2018 - 03:18:10 PST)
Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??)
Bill Ross
(Mon Dec 10 2018 - 03:22:59 PST)
Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??)
Gustaf Olsson
(Mon Dec 10 2018 - 04:32:36 PST)
Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??)
Margarita I. Bernal-Uruchurtu
(Tue Dec 11 2018 - 05:26:28 PST)
Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??)
Margarita I. Bernal-Uruchurtu
(Tue Dec 11 2018 - 05:35:29 PST)
Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??)
Gustaf Olsson
(Tue Dec 11 2018 - 05:41:57 PST)
Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??)
David A Case
(Tue Dec 11 2018 - 10:31:15 PST)
Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??)
Gustaf Olsson
(Mon Dec 17 2018 - 06:21:04 PST)
[AMBER] Size limit for amber
Ibrahim M. Moustafa
(Mon Dec 10 2018 - 09:27:09 PST)
Re: [AMBER] Size limit for amber
David A Case
(Mon Dec 10 2018 - 10:34:30 PST)
Re: [AMBER] Size limit for amber
Ibrahim M. Moustafa
(Mon Dec 10 2018 - 10:44:41 PST)
Re: [AMBER] Size limit for amber
Daniel Roe
(Wed Dec 12 2018 - 08:01:26 PST)
Re: [AMBER] Size limit for amber
Ibrahim M. Moustafa
(Wed Dec 12 2018 - 10:42:14 PST)
[AMBER] amber12 install problem
Qasim Pars
(Mon Dec 10 2018 - 11:46:57 PST)
Re: [AMBER] amber12 install problem
David A Case
(Tue Dec 11 2018 - 04:41:21 PST)
[AMBER] Fatty acid ester parameter file
andreas.tosstorff.cup.uni-muenchen.de
(Mon Dec 10 2018 - 13:28:06 PST)
[AMBER] How to get the jac.restrt？
王茜茜
(Mon Dec 10 2018 - 19:37:04 PST)
[AMBER] Re: How to get the jac.restrt？
Elvis Martis
(Mon Dec 10 2018 - 20:48:15 PST)
Re: [AMBER] How to get the jac.restrt？
王茜茜
(Mon Dec 10 2018 - 22:53:26 PST)
[AMBER] Re: How to get the jac.restrt？
Elvis Martis
(Tue Dec 11 2018 - 00:53:45 PST)
Re: [AMBER] How to get the jac.restrt？
王茜茜
(Tue Dec 11 2018 - 01:08:18 PST)
Re: [AMBER] How to get the jac.restrt？
David A Case
(Tue Dec 11 2018 - 04:46:36 PST)
Re: [AMBER] How to get the jac.restrt？
王茜茜
(Tue Dec 11 2018 - 06:14:24 PST)
[AMBER] Reading Amber-generated NetCDF files using python
Debostuti Ghoshdastidar
(Mon Dec 10 2018 - 23:16:28 PST)
Re: [AMBER] Reading Amber-generated NetCDF files using python
Pratul Agarwal
(Tue Dec 11 2018 - 04:18:26 PST)
Re: [AMBER] Reading Amber-generated NetCDF files using python
Debostuti Ghoshdastidar
(Tue Dec 11 2018 - 04:22:39 PST)
Re: [AMBER] Reading Amber-generated NetCDF files using python
Pratul Agarwal
(Tue Dec 11 2018 - 04:33:57 PST)
Re: [AMBER] Reading Amber-generated NetCDF files using python
Debostuti Ghoshdastidar
(Tue Dec 11 2018 - 22:21:03 PST)
Re: [AMBER] Reading Amber-generated NetCDF files using python
David A Case
(Tue Dec 11 2018 - 04:49:04 PST)
Re: [AMBER] Reading Amber-generated NetCDF files using python
Debostuti Ghoshdastidar
(Tue Dec 11 2018 - 22:17:10 PST)
[AMBER] GBSA error
jacob wick
(Tue Dec 11 2018 - 00:49:15 PST)
[AMBER] GBSA error
jacob wick
(Tue Dec 11 2018 - 21:45:32 PST)
Re: [AMBER] GBSA error
Daniel Roe
(Wed Dec 12 2018 - 08:45:20 PST)
[AMBER] GIST calculation on NAMD-generated trajectory
Bin Sun
(Tue Dec 11 2018 - 11:52:48 PST)
Re: [AMBER] GIST calculation on NAMD-generated trajectory
Daniel Roe
(Wed Dec 12 2018 - 07:58:30 PST)
Re: [AMBER] GIST calculation on NAMD-generated trajectory
anthonycruzpr
(Wed Dec 12 2018 - 15:42:11 PST)
Re: [AMBER] GIST calculation on NAMD-generated trajectory
Daniel Roe
(Wed Dec 12 2018 - 17:40:08 PST)
Re: [AMBER] GIST calculation on NAMD-generated trajectory
Bin Sun
(Thu Dec 13 2018 - 11:55:14 PST)
Re: [AMBER] GIST calculation on NAMD-generated trajectory
Daniel Roe
(Thu Dec 13 2018 - 11:59:00 PST)
Re: [AMBER] GIST calculation on NAMD-generated trajectory
Tom Kurtzman
(Tue Dec 18 2018 - 10:26:27 PST)
Re: [AMBER] GIST calculation on NAMD-generated trajectory
Bin Sun
(Thu Dec 13 2018 - 11:57:19 PST)
[AMBER] PSF file generation for heme and hydrogen peroxide
대학원/일반대학원 생명과학부
(Wed Dec 12 2018 - 18:37:09 PST)
Re: [AMBER] PSF file generation for heme and hydrogen peroxide
David A Case
(Thu Dec 13 2018 - 05:25:10 PST)
[AMBER] strange line between protein chains
Núbia Prates
(Thu Dec 13 2018 - 07:20:42 PST)
Re: [AMBER] strange line between protein chains
Pratul Agarwal
(Thu Dec 13 2018 - 09:25:19 PST)
Re: [AMBER] strange line between protein chains
Núbia Prates
(Fri Dec 14 2018 - 04:54:40 PST)
Re: [AMBER] strange line between protein chains
Pratul Agarwal
(Fri Dec 14 2018 - 12:18:02 PST)
Re: [AMBER] strange line between protein chains
David A Case
(Thu Dec 13 2018 - 09:45:30 PST)
Re: [AMBER] strange line between protein chains
Bill Ross
(Thu Dec 13 2018 - 10:25:55 PST)
[AMBER] mmpbsa
Farial Tavakoli
(Thu Dec 13 2018 - 08:59:04 PST)
[AMBER] using sander in Xeon Phi
Alfredo Quevedo
(Wed Dec 12 2018 - 13:29:12 PST)
Re: [AMBER] using sander in Xeon Phi
David A Case
(Thu Dec 13 2018 - 09:42:41 PST)
Re: [AMBER] using sander in Xeon Phi
Alfredo Quevedo
(Wed Dec 12 2018 - 14:03:07 PST)
[AMBER] Error when installing AMBER16
Bellesis, Andrew G
(Thu Dec 13 2018 - 09:55:38 PST)
[AMBER] sander: command not found
maya nair
(Fri Dec 14 2018 - 04:54:50 PST)
Re: [AMBER] sander: command not found
Gustaf Olsson
(Fri Dec 14 2018 - 05:14:10 PST)
[AMBER] MMPBSA
Farial Tavakoli
(Fri Dec 14 2018 - 07:26:48 PST)
[AMBER] resp charge fitting
Thomas Fox
(Fri Dec 14 2018 - 08:14:41 PST)
[AMBER] AMBER18 on RTX 2080Ti
Rui Sun
(Fri Dec 14 2018 - 14:53:23 PST)
Re: [AMBER] AMBER18 on RTX 2080Ti
David Cerutti
(Fri Dec 14 2018 - 15:09:21 PST)
Re: [AMBER] AMBER18 on RTX 2080Ti
Rui Sun
(Mon Dec 17 2018 - 16:46:59 PST)
Re: [AMBER] AMBER18 on RTX 2080Ti
Pratul Agarwal
(Mon Dec 17 2018 - 17:16:31 PST)
Re: [AMBER] AMBER18 on RTX 2080Ti
Ross Walker
(Mon Dec 17 2018 - 17:55:22 PST)
Re: [AMBER] AMBER18 on RTX 2080Ti
David Cerutti
(Mon Dec 17 2018 - 19:37:48 PST)
Re: [AMBER] AMBER18 on RTX 2080Ti
Rui Sun
(Tue Dec 18 2018 - 02:56:02 PST)
Re: [AMBER] AMBER18 on RTX 2080Ti
Pratul Agarwal
(Tue Dec 18 2018 - 09:43:59 PST)
Re: [AMBER] AMBER18 on RTX 2080Ti
Mlynsky Vojtech
(Fri Dec 21 2018 - 07:25:43 PST)
Re: [AMBER] AMBER18 on RTX 2080Ti
Pratul Agarwal
(Fri Dec 14 2018 - 15:29:57 PST)
Re: [AMBER] AMBER18 on RTX 2080Ti
David Cerutti
(Fri Dec 14 2018 - 18:01:31 PST)
[AMBER] Query regarding force field
Rakesh Srivastava
(Sat Dec 15 2018 - 08:05:19 PST)
Re: [AMBER] Query regarding force field
David Case
(Sat Dec 15 2018 - 18:04:32 PST)
Re: [AMBER] Query regarding force field
Rakesh Srivastava
(Sat Dec 15 2018 - 22:46:30 PST)
[AMBER] Acpype related problem : topology for GROMACS
Seketoulie Keretsu
(Sun Dec 16 2018 - 05:58:08 PST)
Re: [AMBER] Acpype related problem : topology for GROMACS
Bill Ross
(Sun Dec 16 2018 - 06:10:07 PST)
Re: [AMBER] Acpype related problem : topology for GROMACS
Seketoulie Keretsu
(Sun Dec 16 2018 - 16:31:42 PST)
Re: [AMBER] Acpype related problem : topology for GROMACS
Bill Ross
(Sun Dec 16 2018 - 18:48:27 PST)
Re: [AMBER] Acpype related problem : topology for GROMACS
Seketoulie Keretsu
(Sun Dec 16 2018 - 21:11:33 PST)
Re: [AMBER] Acpype related problem : topology for GROMACS
Alan
(Mon Dec 17 2018 - 01:24:12 PST)
Re: [AMBER] Acpype related problem : topology for GROMACS
David A Case
(Mon Dec 17 2018 - 05:13:01 PST)
Re: [AMBER] Acpype related problem : topology for GROMACS
Seketoulie Keretsu
(Mon Dec 17 2018 - 05:20:09 PST)
Re: [AMBER] Acpype related problem : topology for GROMACS
Alan
(Mon Dec 17 2018 - 07:26:36 PST)
Re: [AMBER] Acpype related problem : topology for GROMACS
Seketoulie Keretsu
(Mon Dec 17 2018 - 08:04:12 PST)
[AMBER] DOi for Amber 2017
David Sáez
(Sun Dec 16 2018 - 12:30:41 PST)
Re: [AMBER] DOi for Amber 2017
David A Case
(Mon Dec 17 2018 - 05:13:28 PST)
[AMBER] MCPB.py Modelling Question
Hunter Wilson
(Sun Dec 16 2018 - 12:48:07 PST)
Re: [AMBER] MCPB.py Modelling Question
Pengfei Li
(Fri Dec 21 2018 - 14:21:27 PST)
Re: [AMBER] MCPB.py Modelling Question
Hunter Wilson
(Sat Dec 29 2018 - 14:17:11 PST)
Re: [AMBER] Lipid NMR order parameters
Baker, Joseph
(Sun Dec 16 2018 - 16:59:48 PST)
Re: [AMBER] Lipid NMR order parameters
Daniel Roe
(Fri Dec 21 2018 - 11:46:00 PST)
[AMBER] is acpype compatible with amber 2018?? parmchk2 and not parmchk available
Seketoulie Keretsu
(Sun Dec 16 2018 - 21:07:04 PST)
[AMBER] CUDA test failure
Asma Abro
(Sun Dec 16 2018 - 23:22:47 PST)
Re: [AMBER] CUDA test failure
Bill Ross
(Sun Dec 16 2018 - 23:42:35 PST)
Re: [AMBER] CUDA test failure
David A Case
(Mon Dec 17 2018 - 05:21:33 PST)
Re: [AMBER] CUDA test failure
Pratul Agarwal
(Mon Dec 17 2018 - 06:10:09 PST)
Re: [AMBER] CUDA test failure
Asma Abro
(Mon Dec 17 2018 - 06:33:42 PST)
[AMBER] AMBER16 re-installation problem
ilhan.yavuz
(Mon Dec 17 2018 - 01:06:30 PST)
Re: [AMBER] AMBER16 re-installation problem
David A Case
(Mon Dec 17 2018 - 05:31:09 PST)
[AMBER] Query regarding the internal energy of protein.
Leena Aggarwal
(Mon Dec 17 2018 - 02:09:29 PST)
Re: [AMBER] Query regarding the internal energy of protein.
David A Case
(Mon Dec 17 2018 - 05:34:56 PST)
Re: [AMBER] Query regarding the internal energy of protein.
Pratul Agarwal
(Mon Dec 17 2018 - 07:37:58 PST)
Re: [AMBER] Query regarding the internal energy of protein.
Leena Aggarwal
(Mon Dec 17 2018 - 22:14:46 PST)
[AMBER] lambda option in SEBOMD
Margarita I. Bernal-Uruchurtu
(Mon Dec 17 2018 - 05:15:38 PST)
[AMBER] Problems modifing box lengths in a .rst file.
Lucas Bandeira
(Mon Dec 17 2018 - 08:43:04 PST)
Re: [AMBER] Problems modifing box lengths in a .rst file.
Lucas Bandeira
(Mon Dec 17 2018 - 08:45:46 PST)
Re: [AMBER] Problems modifing box lengths in a .rst file.
Daniel Roe
(Mon Dec 17 2018 - 09:13:53 PST)
Re: [AMBER] Problems modifing box lengths in a .rst file.
Lucas Bandeira
(Mon Dec 17 2018 - 10:18:00 PST)
Re: [AMBER] Problems modifing box lengths in a .rst file.
Daniel Roe
(Mon Dec 17 2018 - 10:59:54 PST)
Re: [AMBER] Problems modifing box lengths in a .rst file.
David A Case
(Tue Dec 18 2018 - 05:18:52 PST)
Re: [AMBER] Problems modifing box lengths in a .rst file.
Lucas Bandeira
(Tue Dec 18 2018 - 07:29:31 PST)
Re: [AMBER] Problems modifing box lengths in a .rst file.
Daniel Roe
(Tue Dec 18 2018 - 09:18:14 PST)
Re: [AMBER] Problems modifing box lengths in a .rst file.
David Cerutti
(Tue Dec 18 2018 - 09:44:56 PST)
Re: [AMBER] Problems modifing box lengths in a .rst file.
Lucas Bandeira
(Wed Dec 19 2018 - 07:25:34 PST)
[AMBER] Missing gaff parameters for epoxy ring
Chang Woon Jang
(Mon Dec 17 2018 - 15:07:09 PST)
Re: [AMBER] Missing gaff parameters for epoxy ring
David A Case
(Tue Dec 18 2018 - 05:21:49 PST)
Re: [AMBER] Missing gaff parameters for epoxy ring
Chang Woon Jang
(Tue Dec 18 2018 - 09:29:23 PST)
[AMBER] amd running error
Nisha Amarnath Jonniya
(Mon Dec 17 2018 - 22:01:20 PST)
Re: [AMBER] amd running error
Gustaf Olsson
(Mon Dec 17 2018 - 23:25:57 PST)
Re: [AMBER] amd running error
Bill Ross
(Mon Dec 17 2018 - 23:52:38 PST)
[AMBER] Too much comparisons failed for test_at_parallel
changseo park
(Tue Dec 18 2018 - 04:07:28 PST)
Re: [AMBER] Too much comparisons failed for test_at_parallel
David A Case
(Tue Dec 18 2018 - 09:15:46 PST)
[AMBER] error on equilibriation
Akshay Prabhakant
(Tue Dec 18 2018 - 07:55:10 PST)
Re: [AMBER] error on equilibriation
Pratul Agarwal
(Tue Dec 18 2018 - 08:09:00 PST)
[AMBER] Simulating a DNA Double helix with a mutated base pair
Anthony Bogetti
(Tue Dec 18 2018 - 08:43:11 PST)
Re: [AMBER] Simulating a DNA Double helix with a mutated base pair
Pratul Agarwal
(Tue Dec 18 2018 - 09:07:55 PST)
Re: [AMBER] Simulating a DNA Double helix with a mutated base pair
David A Case
(Tue Dec 18 2018 - 09:10:33 PST)
[AMBER] info on trajectory files
Akshay Prabhakant
(Wed Dec 19 2018 - 01:14:59 PST)
Re: [AMBER] info on trajectory files
Dr. Anselm Horn
(Wed Dec 19 2018 - 02:12:01 PST)
[AMBER] Problems calculating self diffusion coefficient of water
Lucas Bandeira
(Wed Dec 19 2018 - 09:13:07 PST)
Re: [AMBER] Problems calculating self diffusion coefficient of water
Saeed Izadi
(Wed Dec 19 2018 - 12:52:06 PST)
Re: [AMBER] Problems calculating self diffusion coefficient of water
Lucas Bandeira
(Thu Dec 20 2018 - 02:21:04 PST)
Re: [AMBER] Problems calculating self diffusion coefficient of water
Tom Kurtzman
(Thu Dec 20 2018 - 05:13:30 PST)
Re: [AMBER] Problems calculating self diffusion coefficient of water
Daniel Roe
(Fri Dec 21 2018 - 12:04:39 PST)
Re: [AMBER] Problems calculating self diffusion coefficient of water
Lucas Bandeira
(Sat Dec 22 2018 - 05:30:37 PST)
[AMBER] CUDA bootstrap site
Bill Ross
(Wed Dec 19 2018 - 20:05:59 PST)
[AMBER] cation-pi and amber FF
Sundar
(Wed Dec 19 2018 - 21:36:45 PST)
[AMBER] Amber18 compilation error on a Linux CPU cluster
Sundar
(Wed Dec 19 2018 - 21:47:23 PST)
Re: [AMBER] Amber18 compilation error on a Linux CPU cluster
David A Case
(Thu Dec 20 2018 - 04:54:07 PST)
Re: [AMBER] Amber18 compilation error on a Linux CPU cluster
Sundar
(Sat Dec 22 2018 - 20:21:07 PST)
Re: [AMBER] Amber18 compilation error on a Linux CPU cluster
Sundar
(Sun Dec 23 2018 - 10:40:59 PST)
Re: [AMBER] Amber18 compilation error on a Linux CPU cluster
Bill Ross
(Sun Dec 23 2018 - 11:17:50 PST)
Re: [AMBER] Amber18 compilation error on a Linux CPU cluster
Sundar
(Mon Dec 24 2018 - 17:16:49 PST)
Re: [AMBER] Amber18 compilation error on a Linux CPU cluster
Daniel Roe
(Fri Dec 28 2018 - 06:24:47 PST)
[AMBER] ACE
Keiran Corbett
(Thu Dec 20 2018 - 00:22:58 PST)
Re: [AMBER] ACE
Bill Ross
(Thu Dec 20 2018 - 02:39:23 PST)
Re: [AMBER] ACE
David Cerutti
(Thu Dec 20 2018 - 02:44:02 PST)
Re: [AMBER] ACE
Bill Ross
(Thu Dec 20 2018 - 03:05:42 PST)
[AMBER] Axis of a helix as a collective variable
Akshay Prabhakant
(Thu Dec 20 2018 - 09:13:26 PST)
Re: [AMBER] Axis of a helix as a collective variable
Akshay Prabhakant
(Thu Dec 20 2018 - 09:30:14 PST)
Re: [AMBER] Axis of a helix as a collective variable
Wesley Michael Botello-Smith
(Thu Dec 20 2018 - 10:37:24 PST)
Re: [AMBER] Axis of a helix as a collective variable
Osman, Roman
(Thu Dec 20 2018 - 10:54:03 PST)
Re: [AMBER] Axis of a helix as a collective variable
Pratul Agarwal
(Thu Dec 20 2018 - 12:23:53 PST)
Re: [AMBER] Axis of a helix as a collective variable
Wesley Michael Botello-Smith
(Thu Dec 20 2018 - 15:11:25 PST)
Re: [AMBER] Axis of a helix as a collective variable
Pratul Agarwal
(Thu Dec 20 2018 - 15:19:18 PST)
Re: [AMBER] Axis of a helix as a collective variable
Akshay Prabhakant
(Thu Dec 20 2018 - 19:24:06 PST)
Re: [AMBER] Axis of a helix as a collective variable
Pratul Agarwal
(Thu Dec 20 2018 - 21:35:17 PST)
[AMBER] ff12pol in Amber 18
Han, Jaebeom
(Thu Dec 20 2018 - 12:37:34 PST)
Re: [AMBER] ff12pol in Amber 18
Ray Luo
(Thu Dec 20 2018 - 14:51:45 PST)
[AMBER] mpi
Charu Sharma (JRF)
(Thu Dec 20 2018 - 22:04:44 PST)
Re: [AMBER] mpi
Elvis Martis
(Thu Dec 20 2018 - 22:08:08 PST)
Re: [AMBER] mpi
David A Case
(Fri Dec 21 2018 - 05:57:34 PST)
[AMBER] Total energy of glycan simulation is postive
Rajarshi Roy
(Fri Dec 21 2018 - 03:38:30 PST)
Re: [AMBER] Total energy of glycan simulation is postive
Daniel Roe
(Fri Dec 21 2018 - 05:49:55 PST)
Re: [AMBER] Total energy of glycan simulation is postive
David A Case
(Fri Dec 21 2018 - 06:00:12 PST)
Re: [AMBER] Total energy of glycan simulation is postive
Rajarshi Roy
(Sat Dec 22 2018 - 02:26:38 PST)
[AMBER] cpin file format issue in production run
Manju Sah
(Fri Dec 21 2018 - 03:45:32 PST)
Re: [AMBER] cpin file format issue in production run
Cruzeiro,Vinicius Wilian D
(Fri Dec 21 2018 - 06:58:25 PST)
[AMBER] How to add ff99sb*ildn?
Midhun K Madhu
(Fri Dec 21 2018 - 07:22:33 PST)
Re: [AMBER] How to add ff99sb*ildn?
Vlad Cojocaru
(Fri Dec 21 2018 - 07:43:22 PST)
Re: [AMBER] How to add ff99sb*ildn?
Leena Aggarwal
(Fri Dec 21 2018 - 20:51:50 PST)
[AMBER] Problem running tiMerge (parmed)
Wesley Michael Botello-Smith
(Fri Dec 21 2018 - 09:15:47 PST)
[AMBER] Testing AMBER16 installation in parallel; possible bug in testing scripts
Bellesis, Andrew G
(Fri Dec 21 2018 - 12:56:46 PST)
Re: [AMBER] Testing AMBER16 installation in parallel; possible bug in testing scripts
Pratul Agarwal
(Fri Dec 21 2018 - 15:04:38 PST)
Re: [AMBER] Testing AMBER16 installation in parallel; possible bug in testing scripts
David Case
(Sat Dec 22 2018 - 14:22:54 PST)
[AMBER] multiconformational respgen with fixed charges and gcc 4.8
Stephan Schott
(Sat Dec 22 2018 - 15:39:56 PST)
Re: [AMBER] multiconformational respgen with fixed charges and gcc 4.8
David Case
(Sun Dec 30 2018 - 06:06:28 PST)
Re: [AMBER] multiconformational respgen with fixed charges and gcc 4.8
Stephan Schott
(Sun Dec 30 2018 - 16:38:16 PST)
[AMBER] MD Analysis - Consistency
senal dinuka
(Sat Dec 22 2018 - 22:10:44 PST)
Re: [AMBER] MD Analysis - Consistency
Daniel Roe
(Fri Dec 28 2018 - 06:33:39 PST)
[AMBER] regarding G-quadraplex
Charu Sharma (JRF)
(Mon Dec 24 2018 - 04:31:18 PST)
Re: [AMBER] regarding G-quadraplex
Bill Ross
(Mon Dec 24 2018 - 05:12:36 PST)
[AMBER] constant dieletcric
Farial Tavakoli
(Tue Dec 25 2018 - 05:05:23 PST)
[AMBER] Fwd: constant dieletcric
Farial Tavakoli
(Thu Dec 27 2018 - 22:15:25 PST)
Re: [AMBER] constant dieletcric
Daniel Roe
(Fri Dec 28 2018 - 06:06:51 PST)
[AMBER] All Energy Calculations in AMBER18.
DHEERAJ CHITARA
(Tue Dec 25 2018 - 05:58:19 PST)
Re: [AMBER] All Energy Calculations in AMBER18.
Daniel Roe
(Fri Dec 28 2018 - 06:21:01 PST)
[AMBER] Calculation of Hbond energy
MOHD HOMAIDUR RAHMAN
(Tue Dec 25 2018 - 07:33:58 PST)
Re: [AMBER] Calculation of Hbond energy
David Case
(Tue Dec 25 2018 - 14:42:48 PST)
[AMBER] FATAL Error: Atom does not have a type
Mac Kevin Braza
(Tue Dec 25 2018 - 20:36:55 PST)
[AMBER] Fwd: FATAL Error: Atom does not have a type
Mac Kevin Braza
(Tue Dec 25 2018 - 20:38:01 PST)
Re: [AMBER] FATAL Error: Atom does not have a type
Elvis Martis
(Tue Dec 25 2018 - 20:57:22 PST)
Re: [AMBER] FATAL Error: Atom does not have a type
David Case
(Wed Dec 26 2018 - 18:35:33 PST)
Re: [AMBER] FATAL Error: Atom does not have a type
Mac Kevin Braza
(Thu Dec 27 2018 - 02:58:26 PST)
Re: [AMBER] FATAL Error: Atom does not have a type
Bill Ross
(Thu Dec 27 2018 - 04:07:32 PST)
[AMBER] GPU download(upload) only a small subset of coordinates
张浩淼
(Wed Dec 26 2018 - 01:12:02 PST)
Re: [AMBER] GPU download(upload) only a small subset of coordinates
Ghoreishi, Delaram
(Wed Dec 26 2018 - 10:22:41 PST)
[AMBER] TI method with combination of restrained MD in pmemd.cuda of AMBER18
kegohda2kegohda.mx5.canvas.ne.jp
(Wed Dec 26 2018 - 05:11:59 PST)
Re: [AMBER] TI method with combination of restrained MD in pmemd.cuda of AMBER18
David Case
(Thu Dec 27 2018 - 06:25:54 PST)
Re: [AMBER] TI method with combination of restrained MD in pmemd.cuda of AMBER18
kegohda2kegohda.mx5.canvas.ne.jp
(Fri Dec 28 2018 - 04:41:53 PST)
[AMBER] compilation error AMBER16
Seibold, Steve Allan
(Thu Dec 27 2018 - 11:31:20 PST)
Re: [AMBER] compilation error AMBER16
David Case
(Thu Dec 27 2018 - 12:56:06 PST)
Re: [AMBER] compilation error AMBER16
Seibold, Steve Allan
(Fri Dec 28 2018 - 07:52:56 PST)
[AMBER] q
wangjianing_mail
(Sat Dec 29 2018 - 04:19:24 PST)
[AMBER] HMR 4fs error.
M RCC
(Mon Dec 31 2018 - 02:06:51 PST)
Re: [AMBER] HMR 4fs error.
David A Case
(Mon Dec 31 2018 - 04:49:22 PST)
[AMBER] Obtaining necessary *.top for MMPBSA.py
Sundar
(Mon Dec 31 2018 - 06:08:46 PST)
Re: [AMBER] Obtaining necessary *.top for MMPBSA.py
Qinghua Liao
(Mon Dec 31 2018 - 07:12:16 PST)
Last message date
:
Mon Dec 31 2018 - 07:30:02 PST
Archived on
: Wed Apr 17 2024 - 05:55:38 PDT
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