Amber Archive Jan 2021 by subject
402 messages
:
Starting
Fri Jan 01 2021 - 11:30:02 PST,
Ending
Sun Jan 31 2021 - 12:30:02 PST
sort by
: [
thread
] [
author
] [
date
] [ subject ] [
attachment
]
[AMBER] abfQMMM with Terachem
Eugen Hruska
(Tue Jan 12 2021 - 10:21:06 PST)
[AMBER] abmd ignores cv_min cv_max and resolution for colvar="TORSION"
Feng Pan
(Fri Jan 29 2021 - 12:39:46 PST)
Luis Simon
(Mon Jan 25 2021 - 13:03:43 PST)
[AMBER] Amber 16/cpptraj diffusion command
Daniel Roe
(Mon Jan 25 2021 - 06:11:36 PST)
Pau Mayorga Delgado
(Mon Jan 25 2021 - 00:37:48 PST)
[AMBER] Amber 20 installation, problems with the testing phase
Beatriz Gomes Guimaraes
(Thu Jan 07 2021 - 13:41:27 PST)
David A Case
(Thu Jan 07 2021 - 12:44:27 PST)
Beatriz Gomes Guimaraes
(Thu Jan 07 2021 - 05:21:44 PST)
Beatriz Gomes Guimaraes
(Wed Jan 06 2021 - 08:17:11 PST)
David A Case
(Tue Jan 05 2021 - 19:37:14 PST)
Beatriz Gomes Guimaraes
(Tue Jan 05 2021 - 06:31:46 PST)
David A Case
(Tue Jan 05 2021 - 05:26:19 PST)
Beatriz Gomes Guimaraes
(Mon Jan 04 2021 - 13:20:26 PST)
[AMBER] Amber GPU performance history
David A Case
(Sun Jan 10 2021 - 11:32:01 PST)
[AMBER] Amber20 with PLUMED running slow, with GPU utilisation ~40%
Amanda Buyan
(Tue Jan 12 2021 - 15:36:36 PST)
Adrian Roitberg
(Tue Jan 12 2021 - 09:55:56 PST)
David A Case
(Tue Jan 12 2021 - 09:51:06 PST)
Amanda Buyan
(Mon Jan 11 2021 - 19:24:58 PST)
[AMBER] antechamber assigns DU as atom type for nitrogen
David A Case
(Sat Jan 23 2021 - 14:23:53 PST)
nguerin
(Sat Jan 16 2021 - 19:47:04 PST)
[AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled
Hector A. Baldoni
(Tue Jan 12 2021 - 08:44:05 PST)
Vaibhav Dixit
(Mon Jan 11 2021 - 22:52:25 PST)
David A Case
(Mon Jan 11 2021 - 05:18:40 PST)
Vaibhav Dixit
(Sun Jan 10 2021 - 22:59:49 PST)
[AMBER] Bug in the Mol2 format: space converted into a new oxygen atom
David A Case
(Fri Jan 08 2021 - 07:01:31 PST)
Mateusz Bieniek
(Wed Jan 06 2021 - 06:40:28 PST)
[AMBER] Bug when using RESPA in REMD runs
Charo del Genio
(Sat Jan 30 2021 - 07:51:18 PST)
Carlos Simmerling
(Sat Jan 30 2021 - 07:08:30 PST)
Brian Radak
(Sat Jan 30 2021 - 07:01:45 PST)
David A Case
(Sat Jan 30 2021 - 07:01:26 PST)
Charo del Genio
(Sat Jan 30 2021 - 03:23:41 PST)
[AMBER] Can we perform combined clustering with multiple prmtop files and mdcrd files?
Kenneth Huang
(Fri Jan 29 2021 - 09:51:32 PST)
Debarati DasGupta
(Fri Jan 29 2021 - 06:36:40 PST)
[AMBER] Can't restart a RXSGLD run (possible bug)
Charo del Genio
(Sun Jan 31 2021 - 02:13:41 PST)
[AMBER] cif to pdb
Daniel Roe
(Wed Jan 06 2021 - 02:18:54 PST)
Pinky Mazumder
(Tue Jan 05 2021 - 23:07:49 PST)
David A Case
(Tue Jan 05 2021 - 05:30:30 PST)
Pinky Mazumder
(Mon Jan 04 2021 - 20:19:22 PST)
[AMBER] combining crashed trajectories
Daniel Roe
(Fri Jan 22 2021 - 10:46:45 PST)
Dr. Anselm Horn
(Wed Jan 20 2021 - 09:25:43 PST)
Ayesha Fatima
(Wed Jan 20 2021 - 05:58:19 PST)
[AMBER] Cpptraj
Daniel Roe
(Fri Jan 22 2021 - 09:23:30 PST)
Daniel Roe
(Thu Jan 21 2021 - 07:19:48 PST)
Stejskal, Lenka
(Thu Jan 21 2021 - 07:14:43 PST)
[AMBER] CPPTRAJ error while Clustering
Daniel Roe
(Fri Jan 08 2021 - 09:31:49 PST)
Maghsoud, Yazdan
(Fri Jan 08 2021 - 08:08:27 PST)
[AMBER] Cpptraj v13 command is not working fixatomorder
Daniel Roe
(Mon Jan 11 2021 - 09:43:55 PST)
Ana Ziad
(Sun Jan 10 2021 - 23:01:44 PST)
[AMBER] Creating input files using tleap
Nicy yadav
(Wed Jan 20 2021 - 06:26:08 PST)
David A Case
(Wed Jan 20 2021 - 05:30:06 PST)
Nicy yadav
(Tue Jan 19 2021 - 14:27:00 PST)
[AMBER] Distance of every c alpha in a protein to every other c alpha
Daniel Roe
(Tue Jan 19 2021 - 06:46:07 PST)
Jenny 148
(Sun Jan 17 2021 - 21:50:28 PST)
[AMBER] DNA protein simulation protocol
David A Case
(Mon Jan 25 2021 - 19:11:46 PST)
Airy Sanjeev
(Mon Jan 25 2021 - 01:04:14 PST)
[AMBER] DNA-ligand simulation
Thomas Cheatham
(Thu Jan 14 2021 - 16:41:40 PST)
Kehinde Idowu
(Thu Jan 14 2021 - 16:33:20 PST)
[AMBER] do you know
David A Case
(Sun Jan 03 2021 - 06:16:11 PST)
Gordon Richard Chalmers
(Sun Jan 03 2021 - 04:57:50 PST)
[AMBER] Domain distances using cpptraj
Athena N
(Fri Jan 08 2021 - 23:19:12 PST)
[AMBER] doubt frames simulation
MYRIAN TORRES RICO
(Sat Jan 02 2021 - 06:01:08 PST)
David A Case
(Sat Jan 02 2021 - 05:55:59 PST)
Carlos Simmerling
(Sat Jan 02 2021 - 05:26:24 PST)
MYRIAN TORRES RICO
(Sat Jan 02 2021 - 05:00:50 PST)
[AMBER] Energy Evaluations
Daniel Roe
(Tue Jan 05 2021 - 08:14:15 PST)
Carlos Simmerling
(Tue Jan 05 2021 - 04:37:36 PST)
Matthew Guberman-Pfeffer
(Mon Jan 04 2021 - 20:51:42 PST)
[AMBER] Energy minimization script
raissa.conceicao.bol.com.br
(Fri Jan 22 2021 - 12:14:00 PST)
David A Case
(Fri Jan 22 2021 - 07:22:15 PST)
raissa.conceicao.bol.com.br
(Fri Jan 22 2021 - 05:45:00 PST)
[AMBER] Error in minimization
Carlos Simmerling
(Thu Jan 28 2021 - 13:51:06 PST)
Kehinde Idowu
(Thu Jan 28 2021 - 13:06:05 PST)
[AMBER] Error in the apr.py code - steered MD simulation
Eduardo R. Almeida
(Mon Jan 04 2021 - 19:29:23 PST)
[AMBER] Error in xleap: water molecules
Eduardo R. Almeida
(Sun Jan 10 2021 - 11:13:36 PST)
David A Case
(Sun Jan 10 2021 - 07:45:24 PST)
Eduardo R. Almeida
(Sat Jan 09 2021 - 19:02:21 PST)
Bill Ross
(Sat Jan 09 2021 - 18:31:13 PST)
David A Case
(Sat Jan 09 2021 - 18:25:13 PST)
Bill Ross
(Sat Jan 09 2021 - 15:52:54 PST)
Eduardo R. Almeida
(Sat Jan 09 2021 - 15:44:17 PST)
Bill Ross
(Sat Jan 09 2021 - 15:31:41 PST)
Eduardo R. Almeida
(Sat Jan 09 2021 - 15:29:40 PST)
Bill Ross
(Sat Jan 09 2021 - 13:37:22 PST)
David A Case
(Sat Jan 09 2021 - 13:10:50 PST)
Bill Ross
(Sat Jan 09 2021 - 09:30:56 PST)
Eduardo R. Almeida
(Sat Jan 09 2021 - 06:42:19 PST)
David A Case
(Sat Jan 09 2021 - 05:51:19 PST)
Bill Ross
(Fri Jan 08 2021 - 20:43:00 PST)
Eduardo R. Almeida
(Fri Jan 08 2021 - 15:39:20 PST)
[AMBER] error job
MYRIAN TORRES RICO
(Thu Jan 14 2021 - 00:36:31 PST)
Carlos Simmerling
(Wed Jan 13 2021 - 04:40:21 PST)
MYRIAN TORRES RICO
(Tue Jan 12 2021 - 09:20:44 PST)
Carlos Simmerling
(Tue Jan 12 2021 - 07:41:44 PST)
MYRIAN TORRES RICO
(Tue Jan 12 2021 - 07:10:57 PST)
Carlos Simmerling
(Tue Jan 12 2021 - 06:51:34 PST)
MYRIAN TORRES RICO
(Tue Jan 12 2021 - 06:38:11 PST)
David A Case
(Tue Jan 12 2021 - 05:25:58 PST)
MYRIAN TORRES RICO
(Tue Jan 12 2021 - 01:02:25 PST)
David A Case
(Mon Jan 11 2021 - 05:26:09 PST)
MYRIAN TORRES RICO
(Mon Jan 11 2021 - 03:09:58 PST)
[AMBER] Error searching for compatible GPU
Hongwei Tan
(Sun Jan 10 2021 - 16:50:33 PST)
David A Case
(Sun Jan 10 2021 - 07:35:50 PST)
Hongwei Tan
(Sun Jan 10 2021 - 00:29:22 PST)
[AMBER] Error while clustering on CPPTRAJ
Daniel Roe
(Tue Jan 19 2021 - 10:03:31 PST)
Daniel Fernández Remacha
(Tue Jan 19 2021 - 09:50:24 PST)
Daniel Roe
(Tue Jan 19 2021 - 09:39:31 PST)
dnlfr1994.gmail.com
(Tue Jan 19 2021 - 09:20:52 PST)
Daniel Roe
(Thu Jan 14 2021 - 15:58:44 PST)
dnlfr1994.gmail.com
(Thu Jan 14 2021 - 09:50:22 PST)
Daniel Roe
(Thu Jan 14 2021 - 07:51:32 PST)
dnlfr1994.gmail.com
(Thu Jan 14 2021 - 05:03:45 PST)
[AMBER] error...
Carlos Simmerling
(Mon Jan 04 2021 - 05:38:24 PST)
MYRIAN TORRES RICO
(Mon Jan 04 2021 - 02:09:35 PST)
Carlos Simmerling
(Sun Jan 03 2021 - 13:29:47 PST)
Bill Ross
(Sun Jan 03 2021 - 13:14:18 PST)
MYRIAN TORRES RICO
(Sun Jan 03 2021 - 11:43:56 PST)
Bill Ross
(Sun Jan 03 2021 - 11:07:33 PST)
MYRIAN TORRES RICO
(Sun Jan 03 2021 - 09:19:00 PST)
[AMBER] Errors whilst installing GPU Amber20
Victoria E Hill
(Wed Jan 13 2021 - 09:41:58 PST)
tluchko
(Wed Jan 13 2021 - 09:06:03 PST)
Victoria E Hill
(Wed Jan 13 2021 - 09:05:35 PST)
David A Case
(Wed Jan 13 2021 - 05:37:13 PST)
Victoria E Hill
(Wed Jan 13 2021 - 03:58:43 PST)
[AMBER] Extending DNA structure
Airy Sanjeev
(Tue Jan 19 2021 - 02:00:55 PST)
Vlad Cojocaru
(Tue Jan 19 2021 - 01:39:58 PST)
Airy Sanjeev
(Mon Jan 18 2021 - 19:57:16 PST)
[AMBER] ff15ipq-m force field for protein mimetics
Lillian Chong
(Tue Jan 12 2021 - 05:46:41 PST)
[AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card
Setyanto Md
(Sun Jan 03 2021 - 23:47:14 PST)
liu kai
(Sat Jan 02 2021 - 18:35:20 PST)
Mohd Farid Ismail
(Fri Jan 01 2021 - 16:54:56 PST)
[AMBER] Found bug in sander in restarting SGLD replica exchange runs
Charo del Genio
(Sun Jan 31 2021 - 04:35:28 PST)
[AMBER] Fwd: copper RISM
angad sharma
(Wed Jan 06 2021 - 06:13:38 PST)
[AMBER] Fwd: Creating a bond in leap
Kenneth Huang
(Mon Jan 11 2021 - 14:03:23 PST)
Victoria E Hill
(Mon Jan 11 2021 - 13:37:33 PST)
[AMBER] Fwd: Distance of every c alpha in a protein to every other c alpha
Daniel Roe
(Mon Jan 25 2021 - 06:16:32 PST)
Jenny 148
(Mon Jan 25 2021 - 02:11:00 PST)
[AMBER] Fwd: Domain distances using cpptraj
David A Case
(Sun Jan 10 2021 - 05:23:03 PST)
Athena N
(Sat Jan 09 2021 - 20:15:28 PST)
[AMBER] Fwd: Error during amber16 installation
David A Case
(Fri Jan 22 2021 - 07:17:02 PST)
spss4.iacs.res.in
(Thu Jan 21 2021 - 20:59:09 PST)
David A Case
(Thu Jan 21 2021 - 05:16:12 PST)
spss4.iacs.res.in
(Thu Jan 21 2021 - 02:29:46 PST)
[AMBER] gaff/parm
MYRIAN TORRES RICO
(Thu Jan 14 2021 - 05:50:01 PST)
David A Case
(Thu Jan 14 2021 - 05:34:07 PST)
MYRIAN TORRES RICO
(Thu Jan 14 2021 - 01:36:10 PST)
[AMBER] GB pairwise decomposition - Salt Bridge
Carlos Simmerling
(Wed Jan 06 2021 - 06:49:36 PST)
Tarsis
(Wed Jan 06 2021 - 06:28:57 PST)
[AMBER] Generating LJ paramters of divalent copper ions
David A Case
(Sun Jan 03 2021 - 06:09:27 PST)
angad sharma
(Sat Jan 02 2021 - 10:15:43 PST)
[AMBER] Help to generate prmtop and .crd files from a PDB trajectory
Daniel Roe
(Thu Jan 28 2021 - 07:03:28 PST)
Kenneth Huang
(Tue Jan 26 2021 - 11:55:43 PST)
Devlina Chakravarty
(Mon Jan 25 2021 - 17:46:03 PST)
[AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions?
Hector A. Baldoni
(Wed Jan 06 2021 - 19:11:18 PST)
Eduardo R. Almeida
(Wed Jan 06 2021 - 19:05:49 PST)
Bill Ross
(Wed Jan 06 2021 - 18:59:35 PST)
Bill Ross
(Wed Jan 06 2021 - 18:56:01 PST)
Eduardo R. Almeida
(Wed Jan 06 2021 - 18:37:00 PST)
Bill Ross
(Wed Jan 06 2021 - 18:24:57 PST)
Eduardo R. Almeida
(Wed Jan 06 2021 - 18:18:58 PST)
Bill Ross
(Wed Jan 06 2021 - 18:03:59 PST)
Eduardo R. Almeida
(Wed Jan 06 2021 - 17:33:46 PST)
Eduardo R. Almeida
(Wed Jan 06 2021 - 17:28:27 PST)
Bill Ross
(Wed Jan 06 2021 - 17:08:11 PST)
Bill Ross
(Wed Jan 06 2021 - 17:06:34 PST)
Eduardo R. Almeida
(Wed Jan 06 2021 - 15:15:55 PST)
[AMBER] How to apply Compressive loading on wood
Pinky Mazumder
(Sat Jan 16 2021 - 18:55:54 PST)
[AMBER] How to apply GLYCAM Parameters
Matthew Guberman-Pfeffer
(Sun Jan 03 2021 - 12:45:07 PST)
[AMBER] How to apply shear loading on carbohydrates
Pinky Mazumder
(Fri Jan 08 2021 - 21:11:18 PST)
[AMBER] How to extract restart file with velocity from a trajectory file?
Carlos Simmerling
(Fri Jan 22 2021 - 09:32:11 PST)
辛志宏
(Fri Jan 22 2021 - 06:19:42 PST)
[AMBER] How to fix the issue of generating restart file from a trajectory?
Daniel Roe
(Thu Jan 28 2021 - 07:10:41 PST)
辛志宏
(Wed Jan 27 2021 - 20:00:04 PST)
[AMBER] how to get amber 18 tools
David A Case
(Wed Jan 27 2021 - 12:09:44 PST)
Sadaf Rani
(Wed Jan 27 2021 - 06:44:55 PST)
Carlos Simmerling
(Wed Jan 27 2021 - 06:10:59 PST)
Sadaf Rani
(Wed Jan 27 2021 - 04:25:11 PST)
[AMBER] how to pull group of atoms towards a fixed molecule using Steered molecular dynamics simulation
Pinky Mazumder
(Fri Jan 08 2021 - 17:11:43 PST)
[AMBER] How to pull two group of atoms in two different direction?
Pinky Mazumder
(Sun Jan 24 2021 - 16:23:33 PST)
[AMBER] How to pull/push group of atoms
Pinky Mazumder
(Sat Jan 09 2021 - 21:06:06 PST)
[AMBER] How to use AM1 for Ti atom in Amber?
David A Case
(Mon Jan 11 2021 - 05:32:54 PST)
孙天宇
(Sun Jan 10 2021 - 21:28:23 PST)
[AMBER] How to use GLYCAM_06j-1 in LAMMPS
Pinky Mazumder
(Sat Jan 16 2021 - 13:35:18 PST)
David A Case
(Sat Jan 16 2021 - 06:44:04 PST)
Pinky Mazumder
(Fri Jan 15 2021 - 15:43:05 PST)
[AMBER] in chimera, which one should I use for carbohydrates
David A Case
(Fri Jan 29 2021 - 09:32:23 PST)
Pinky Mazumder
(Fri Jan 29 2021 - 07:38:28 PST)
[AMBER] Issue about the generaton of rst files
Daniel Roe
(Tue Jan 12 2021 - 06:28:48 PST)
辛志宏
(Tue Jan 12 2021 - 04:33:44 PST)
Daniel Roe
(Mon Jan 11 2021 - 09:42:02 PST)
辛志宏
(Sun Jan 10 2021 - 06:41:11 PST)
[AMBER] Langevin thermostat different gamma_ln giving systematically different energies?
Thomas Cheatham
(Sat Jan 16 2021 - 18:23:48 PST)
Liao
(Sat Jan 16 2021 - 17:44:16 PST)
[AMBER] Lateral movement of membrane bound protein during MD simulation in Amber
Stephan Schott
(Mon Jan 11 2021 - 03:21:37 PST)
Biplab Ghosh
(Sun Jan 10 2021 - 21:27:36 PST)
[AMBER] LEaP Error/questions.
Sam Walsworth (Researcher)
(Fri Jan 15 2021 - 12:58:57 PST)
David A Case
(Fri Jan 15 2021 - 12:41:17 PST)
Sam Walsworth (Researcher)
(Fri Jan 15 2021 - 10:58:38 PST)
David A Case
(Thu Jan 14 2021 - 14:15:21 PST)
Sam Walsworth (Researcher)
(Wed Jan 13 2021 - 12:41:01 PST)
David A Case
(Wed Jan 13 2021 - 08:11:59 PST)
Sam Walsworth (Researcher)
(Wed Jan 13 2021 - 07:06:44 PST)
Carlos Simmerling
(Wed Jan 13 2021 - 06:44:49 PST)
Sam Walsworth (Researcher)
(Wed Jan 13 2021 - 06:38:33 PST)
Carlos Simmerling
(Wed Jan 13 2021 - 06:13:08 PST)
Daniel Roe
(Wed Jan 13 2021 - 06:11:24 PST)
Sam Walsworth (Researcher)
(Wed Jan 13 2021 - 05:27:55 PST)
Carlos Simmerling
(Wed Jan 13 2021 - 04:37:09 PST)
Sam Walsworth (Researcher)
(Wed Jan 13 2021 - 04:30:36 PST)
David A Case
(Tue Jan 12 2021 - 05:21:37 PST)
David A Case
(Tue Jan 12 2021 - 05:17:15 PST)
Sam Walsworth (Researcher)
(Tue Jan 12 2021 - 05:11:39 PST)
Carlos Simmerling
(Tue Jan 12 2021 - 05:05:01 PST)
Sam Walsworth (Researcher)
(Tue Jan 12 2021 - 04:18:08 PST)
Carlos Simmerling
(Mon Jan 11 2021 - 14:09:33 PST)
Sam Walsworth (Researcher)
(Mon Jan 11 2021 - 12:58:04 PST)
Maria Nagan
(Mon Jan 11 2021 - 09:37:46 PST)
Carlos Simmerling
(Mon Jan 11 2021 - 09:29:29 PST)
Sam Walsworth (Researcher)
(Mon Jan 11 2021 - 09:10:26 PST)
David A Case
(Mon Jan 11 2021 - 08:44:16 PST)
Sam Walsworth (Researcher)
(Mon Jan 11 2021 - 05:45:18 PST)
David A Case
(Mon Jan 11 2021 - 05:29:47 PST)
Sam Walsworth (Researcher)
(Mon Jan 11 2021 - 03:45:14 PST)
[AMBER] lj1264 in vacuum
Pengfei Li
(Sat Jan 16 2021 - 19:21:56 PST)
[AMBER] Major Cpptraj Update (GitHub)
Daniel Roe
(Wed Jan 20 2021 - 11:54:44 PST)
[AMBER] makedepend for sander
Antoine MARION
(Wed Jan 20 2021 - 06:14:04 PST)
David A Case
(Wed Jan 20 2021 - 05:09:43 PST)
Antoine MARION
(Wed Jan 20 2021 - 03:26:06 PST)
[AMBER] max pairlist cutoff must be less than unit cell max sphere radius!
Pinky Mazumder
(Thu Jan 28 2021 - 10:31:52 PST)
David A Case
(Thu Jan 28 2021 - 07:07:32 PST)
Pinky Mazumder
(Wed Jan 27 2021 - 13:49:22 PST)
[AMBER] MD GPU Scaling Performance
David A Case
(Fri Jan 08 2021 - 06:47:42 PST)
Jatin Kashyap
(Thu Jan 07 2021 - 14:38:26 PST)
[AMBER] Missing Iron (Fe) DFTB3 parameters for QM/MM simulation of Enzyme
Goetz, Andreas
(Tue Jan 12 2021 - 16:15:54 PST)
[AMBER] MMPBSA calculation cpptraj failed with ligand prmtop
Sadaf Rani
(Sun Jan 24 2021 - 21:03:10 PST)
Sadaf Rani
(Sun Jan 24 2021 - 20:47:03 PST)
Elvis A F Martis
(Wed Jan 20 2021 - 23:52:57 PST)
Sadaf Rani
(Wed Jan 20 2021 - 21:13:09 PST)
[AMBER] MMPBSA.py.MPI not build in Amber20
Li,Haoxi
(Fri Jan 08 2021 - 14:05:16 PST)
Elvis A F Martis
(Fri Jan 08 2021 - 07:35:44 PST)
David A Case
(Fri Jan 08 2021 - 07:10:57 PST)
Elvis A F Martis
(Mon Jan 04 2021 - 09:19:43 PST)
Li,Haoxi
(Mon Jan 04 2021 - 09:13:32 PST)
[AMBER] NaN VDWAALS Error During Minimization
Jatin Kashyap
(Thu Jan 07 2021 - 11:29:05 PST)
Bill Ross
(Wed Jan 06 2021 - 00:48:17 PST)
David Cerutti
(Tue Jan 05 2021 - 22:36:39 PST)
Jatin Kashyap
(Tue Jan 05 2021 - 22:28:52 PST)
Bill Ross
(Tue Jan 05 2021 - 21:51:28 PST)
Jatin Kashyap
(Tue Jan 05 2021 - 21:09:59 PST)
Thomas Cheatham
(Tue Jan 05 2021 - 20:39:56 PST)
Thomas Cheatham
(Tue Jan 05 2021 - 20:33:17 PST)
Bill Ross
(Tue Jan 05 2021 - 20:01:06 PST)
Bill Ross
(Tue Jan 05 2021 - 19:59:23 PST)
Jatin Kashyap
(Tue Jan 05 2021 - 19:53:29 PST)
Bill Ross
(Tue Jan 05 2021 - 19:45:56 PST)
David A Case
(Tue Jan 05 2021 - 19:44:39 PST)
Jatin Kashyap
(Tue Jan 05 2021 - 19:18:47 PST)
Bill Ross
(Tue Jan 05 2021 - 19:05:23 PST)
David Cerutti
(Tue Jan 05 2021 - 17:29:19 PST)
Jatin Kashyap
(Tue Jan 05 2021 - 16:55:17 PST)
[AMBER] Non zero ligand warning
Kenneth Huang
(Sun Jan 31 2021 - 10:14:48 PST)
David A Case
(Sun Jan 31 2021 - 06:24:59 PST)
Ayesha Fatima
(Sun Jan 31 2021 - 05:10:51 PST)
[AMBER] Non-integer/zero charges from RESP fitting?
Kenneth Huang
(Wed Jan 13 2021 - 10:50:29 PST)
David A Case
(Wed Jan 13 2021 - 05:15:17 PST)
Kenneth Huang
(Tue Jan 12 2021 - 11:18:04 PST)
[AMBER] NonUniversalWarning: Modified off-diagonal LJ parameters detected
David A Case
(Sat Jan 16 2021 - 11:22:39 PST)
Loki
(Sat Jan 16 2021 - 09:30:12 PST)
David A Case
(Sat Jan 16 2021 - 06:45:31 PST)
Loki
(Sat Jan 16 2021 - 03:54:54 PST)
[AMBER] Number of na, cl ions
David A Case
(Thu Jan 14 2021 - 14:08:49 PST)
Женя Елизарова
(Thu Jan 14 2021 - 08:10:11 PST)
[AMBER] Nvidia RTX 3080/3090 Servers
mish
(Fri Jan 22 2021 - 06:16:34 PST)
Ross Walker
(Fri Jan 22 2021 - 06:03:53 PST)
mish
(Thu Jan 21 2021 - 18:48:54 PST)
[AMBER] OPC monovalent ion parameters
Carlos Simmerling
(Mon Jan 25 2021 - 12:35:11 PST)
Sebastian Oleksy
(Mon Jan 25 2021 - 10:07:26 PST)
[AMBER] overall and internal correlation function
Mani Radh
(Mon Jan 25 2021 - 09:48:12 PST)
[AMBER] Patches to fix the replica exchange restart bug
Charo del Genio
(Sun Jan 31 2021 - 12:11:59 PST)
[AMBER] pdb4amber error
David A Case
(Wed Jan 27 2021 - 05:14:14 PST)
Scott Brozell
(Tue Jan 26 2021 - 22:37:06 PST)
Nicy yadav
(Mon Jan 25 2021 - 08:24:33 PST)
[AMBER] Potential energy discrepancy in RXSGLD
Charo del Genio
(Fri Jan 29 2021 - 08:28:51 PST)
[AMBER] Preparation of input file for RAMD (Geng Dong)
东庚
(Sun Jan 10 2021 - 20:11:12 PST)
[AMBER] PrmtopError: Complex natom != receptor natom + ligand natom
David A Case
(Tue Jan 26 2021 - 11:19:55 PST)
Renato Araujo
(Tue Jan 26 2021 - 08:56:11 PST)
David A Case
(Mon Jan 25 2021 - 19:17:14 PST)
Renato Araujo
(Mon Jan 25 2021 - 17:49:58 PST)
[AMBER] Problem in running cmake
Airy Sanjeev
(Mon Jan 11 2021 - 19:01:15 PST)
David A Case
(Mon Jan 11 2021 - 05:23:31 PST)
Airy Sanjeev
(Sun Jan 10 2021 - 23:17:00 PST)
[AMBER] Problem with cudaMalloc GpuBuffer Allocate failed out of memory
Elvis A F Martis
(Fri Jan 01 2021 - 20:36:06 PST)
assawin daducale
(Fri Jan 01 2021 - 11:07:25 PST)
[AMBER] Problem with PB calculation
CAVALLARO MATTIA
(Sat Jan 02 2021 - 06:24:20 PST)
[AMBER] Problems when running make test.parallel
Beatriz Gomes Guimaraes
(Mon Jan 18 2021 - 10:53:18 PST)
Daniel Roe
(Tue Jan 12 2021 - 08:58:14 PST)
Beatriz Gomes Guimaraes
(Tue Jan 12 2021 - 06:35:36 PST)
[AMBER] Probmlems compiling under macOS
Gustaf Olsson
(Wed Jan 13 2021 - 22:32:01 PST)
David A Case
(Mon Jan 11 2021 - 05:11:29 PST)
Gustaf Olsson
(Sun Jan 10 2021 - 13:37:31 PST)
Gustaf Olsson
(Sun Jan 10 2021 - 09:24:07 PST)
David A Case
(Sun Jan 10 2021 - 05:46:50 PST)
Gustaf Olsson
(Sun Jan 10 2021 - 00:13:00 PST)
[AMBER] PROTEIN-DNA rmsd plot
Syeda Amna Arshi
(Mon Jan 04 2021 - 22:23:40 PST)
Daniel Roe
(Mon Jan 04 2021 - 06:09:10 PST)
David A Case
(Mon Jan 04 2021 - 05:19:42 PST)
Syeda Amna Arshi
(Mon Jan 04 2021 - 00:56:57 PST)
[AMBER] PROTEIN-DNA RMSD plots
Dr. Anselm Horn
(Thu Jan 14 2021 - 04:55:59 PST)
Carlos Simmerling
(Thu Jan 14 2021 - 03:22:06 PST)
Syeda Amna Arshi
(Thu Jan 14 2021 - 03:14:05 PST)
[AMBER] Pull group of atoms together
Pinky Mazumder
(Tue Jan 12 2021 - 11:59:22 PST)
Carlos Simmerling
(Tue Jan 12 2021 - 11:43:09 PST)
Pinky Mazumder
(Tue Jan 12 2021 - 11:30:16 PST)
Carlos Simmerling
(Tue Jan 12 2021 - 11:25:42 PST)
Pinky Mazumder
(Tue Jan 12 2021 - 08:38:42 PST)
Carlos Simmerling
(Mon Jan 11 2021 - 10:43:19 PST)
Pinky Mazumder
(Mon Jan 11 2021 - 10:34:11 PST)
[AMBER] Python Error in MMPBSA.py, only for PBSA on final output
Lennart Gundelach
(Fri Jan 22 2021 - 04:22:07 PST)
Ray Luo
(Sat Jan 16 2021 - 17:48:43 PST)
Lennart Gundelach
(Sat Jan 16 2021 - 02:14:54 PST)
Ray Luo
(Wed Jan 13 2021 - 09:10:46 PST)
Lennart Gundelach
(Wed Jan 13 2021 - 01:43:07 PST)
[AMBER] pytraj in python 3.9
Abdul-Rashid III Sampaco
(Wed Jan 06 2021 - 19:53:50 PST)
David A Case
(Wed Jan 06 2021 - 06:29:39 PST)
Abdul-Rashid III Sampaco
(Tue Jan 05 2021 - 20:54:53 PST)
[AMBER] question
David A Case
(Thu Jan 21 2021 - 05:19:27 PST)
MYRIAN TORRES RICO
(Thu Jan 21 2021 - 03:05:45 PST)
[AMBER] Question of targeted molecular dynamics simulation
Dr. Anselm Horn
(Fri Jan 15 2021 - 09:14:18 PST)
吴晓东
(Thu Jan 14 2021 - 18:37:16 PST)
[AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation
Carlos Simmerling
(Mon Jan 18 2021 - 18:02:55 PST)
Jatin Kashyap
(Mon Jan 18 2021 - 17:40:11 PST)
Carlos Simmerling
(Mon Jan 18 2021 - 17:12:30 PST)
Jatin Kashyap
(Mon Jan 18 2021 - 16:48:50 PST)
Roitberg,Adrian E
(Mon Jan 18 2021 - 16:40:00 PST)
Jatin Kashyap
(Mon Jan 18 2021 - 16:06:35 PST)
Carlos Simmerling
(Mon Jan 18 2021 - 16:01:25 PST)
Jatin Kashyap
(Mon Jan 18 2021 - 15:47:58 PST)
Carlos Simmerling
(Mon Jan 18 2021 - 15:43:41 PST)
Jatin Kashyap
(Mon Jan 18 2021 - 15:32:45 PST)
Carlos Simmerling
(Mon Jan 18 2021 - 15:28:15 PST)
Jatin Kashyap
(Mon Jan 18 2021 - 15:17:02 PST)
[AMBER] RMSD analysis
Daniel Roe
(Fri Jan 08 2021 - 13:09:54 PST)
Carlos Simmerling
(Thu Jan 07 2021 - 17:55:01 PST)
K Jan
(Thu Jan 07 2021 - 15:26:14 PST)
Kenneth Huang
(Thu Jan 07 2021 - 14:45:09 PST)
K Jan
(Thu Jan 07 2021 - 14:34:51 PST)
[AMBER] rotdif analysis in cpptraj
Adeleh Mokhles Gerami
(Wed Jan 27 2021 - 06:41:02 PST)
[AMBER] Running simulations
David A Case
(Tue Jan 26 2021 - 11:24:03 PST)
richa anand
(Sun Jan 24 2021 - 22:41:53 PST)
[AMBER] Sander code doesn’t output trajectory files
K Jan
(Wed Jan 06 2021 - 07:13:49 PST)
Roitberg,Adrian E
(Wed Jan 06 2021 - 07:00:44 PST)
K Jan
(Wed Jan 06 2021 - 06:57:16 PST)
David A Case
(Wed Jan 06 2021 - 06:34:44 PST)
Carlos Simmerling
(Wed Jan 06 2021 - 06:25:48 PST)
K Jan
(Wed Jan 06 2021 - 04:58:23 PST)
[AMBER] Setting PME cutoff in Crystal Simulations
David A Case
(Wed Jan 06 2021 - 06:22:13 PST)
Matthew Guberman-Pfeffer
(Wed Jan 06 2021 - 00:33:05 PST)
Matthew Guberman-Pfeffer
(Tue Jan 05 2021 - 19:03:59 PST)
David A Case
(Tue Jan 05 2021 - 05:35:13 PST)
Matthew Guberman-Pfeffer
(Tue Jan 05 2021 - 01:37:22 PST)
David A Case
(Mon Jan 04 2021 - 05:14:34 PST)
Matthew Guberman-Pfeffer
(Sun Jan 03 2021 - 12:37:09 PST)
[AMBER] SMD & MULTI_RMSD
Feng Pan
(Mon Jan 11 2021 - 12:11:07 PST)
Fabian Glaser
(Mon Jan 11 2021 - 06:19:10 PST)
Feng Pan
(Tue Jan 05 2021 - 06:43:15 PST)
Fabian Glaser
(Sun Jan 03 2021 - 13:09:16 PST)
Feng Pan
(Sun Jan 03 2021 - 12:50:54 PST)
Fabian Glaser
(Sun Jan 03 2021 - 09:47:21 PST)
[AMBER] Spam purewater keyword
Debarati DasGupta
(Mon Jan 11 2021 - 12:49:02 PST)
[AMBER] Steered molecular dynamics Simulation
Pinky Mazumder
(Sat Jan 16 2021 - 13:37:28 PST)
Pinky Mazumder
(Sat Jan 16 2021 - 10:13:35 PST)
Fabian Glaser
(Sat Jan 16 2021 - 06:56:04 PST)
Pinky Mazumder
(Fri Jan 15 2021 - 18:01:53 PST)
[AMBER] Suggestions on crossing energy barrier to break strong HBs
Kenneth Huang
(Sat Jan 30 2021 - 17:10:10 PST)
Amit Sharma (Asstt. Prof., MCARS)
(Fri Jan 29 2021 - 22:27:43 PST)
David A Case
(Fri Jan 29 2021 - 19:06:00 PST)
Amit Sharma (Asstt. Prof., MCARS)
(Fri Jan 29 2021 - 15:40:35 PST)
[AMBER] technical problems with installing amber20
David A Case
(Thu Jan 28 2021 - 07:05:06 PST)
Игорь Злотников
(Wed Jan 27 2021 - 12:29:34 PST)
David A Case
(Wed Jan 27 2021 - 12:21:43 PST)
Игорь Злотников
(Wed Jan 27 2021 - 04:59:02 PST)
[AMBER] The long and winding STSM
Feng Pan
(Fri Jan 29 2021 - 12:37:48 PST)
Luis Simon
(Wed Jan 20 2021 - 07:56:33 PST)
[AMBER] TI simulation blowing up with pmemd.CUDA
Debarati DasGupta
(Mon Jan 11 2021 - 09:41:36 PST)
Debarati DasGupta
(Mon Jan 11 2021 - 07:27:22 PST)
Debarati DasGupta
(Mon Jan 11 2021 - 05:52:01 PST)
David A Case
(Mon Jan 11 2021 - 05:09:12 PST)
Delwakkada Liyanage, Senal Dinuka
(Sun Jan 10 2021 - 12:08:21 PST)
David A Case
(Sun Jan 10 2021 - 11:28:09 PST)
Delwakkada Liyanage, Senal Dinuka
(Sun Jan 10 2021 - 10:07:39 PST)
[AMBER] tinker_to_amber
David A Case
(Fri Jan 08 2021 - 06:57:54 PST)
Юлия Беляева
(Tue Jan 05 2021 - 11:16:01 PST)
[AMBER] Tri-coordination environment in zinc
Pengfei Li
(Sat Jan 16 2021 - 19:29:17 PST)
[AMBER] Typo in update.13 for AmberTools20
Hashemi, Mohtadin
(Fri Jan 15 2021 - 12:28:26 PST)
[AMBER] Understanding File Format Specifications
Thomas Cheatham
(Fri Jan 22 2021 - 14:03:52 PST)
nguerin
(Fri Jan 22 2021 - 12:48:45 PST)
[AMBER] US or SMD for torsion angle steering?
Feng Pan
(Tue Jan 12 2021 - 06:35:32 PST)
Fabian Glaser
(Mon Jan 11 2021 - 06:31:08 PST)
[AMBER] vlimit exceeded for step 0; vmax = 50.6241
Pinky Mazumder
(Tue Jan 19 2021 - 13:50:09 PST)
[AMBER] working with mmpbsa with protein and three ligands in same complex
Sadaf Rani
(Tue Jan 19 2021 - 22:42:20 PST)
David A Case
(Sun Jan 17 2021 - 07:16:54 PST)
Sadaf Rani
(Sun Jan 17 2021 - 02:36:31 PST)
[AMBER] ZAFF force field
Tabassum Khair Barbhuiya
(Wed Jan 20 2021 - 17:09:11 PST)
Last message date
:
Sun Jan 31 2021 - 12:30:02 PST
Archived on
: Wed Dec 04 2024 - 05:56:01 PST
402 messages
sort by
: [
thread
] [
author
] [
date
] [ subject ] [
attachment
]
Custom Search