Amber Archive Sep 2018 by thread
284 messages
:
Starting
Fri Aug 31 2018 - 20:30:02 PDT,
Ending
Sat Sep 29 2018 - 11:00:03 PDT
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[AMBER] KDE analysis, (P) greater than one
Mac Kevin Braza
(Fri Aug 31 2018 - 20:24:19 PDT)
Re: [AMBER] KDE analysis, (P) greater than one
Daniel Roe
(Sat Sep 01 2018 - 05:48:25 PDT)
Re: [AMBER] KDE analysis, (P) greater than one
Adrian Roitberg
(Mon Sep 03 2018 - 06:34:24 PDT)
Re: [AMBER] KDE analysis, (P) greater than one
Mac Kevin Braza
(Mon Sep 03 2018 - 18:25:25 PDT)
Re: [AMBER] KDE analysis, (P) greater than one
Jason Swails
(Wed Sep 05 2018 - 20:49:34 PDT)
[AMBER] Constant velocity pulling in SMD
M RCC
(Fri Aug 31 2018 - 23:49:50 PDT)
[AMBER] Temperature calculaton by CPPTRAJ
Ikuo KURISAKI
(Sat Sep 01 2018 - 01:34:48 PDT)
Re: [AMBER] Temperature calculaton by CPPTRAJ
Daniel Roe
(Sat Sep 01 2018 - 05:46:25 PDT)
Re: [AMBER] NCSU_SMD for protein-ligand complex pulling
M RCC
(Sat Sep 01 2018 - 03:25:20 PDT)
[AMBER] Temperature calculaton by CPPTRAJ
Ikuo KURISAKI
(Sat Sep 01 2018 - 03:32:08 PDT)
Re: [AMBER] Temperature calculaton by CPPTRAJ
Ikuo KURISAKI
(Mon Sep 03 2018 - 06:38:34 PDT)
[AMBER] Constant pH and Redox Potential MD tutorial
Cruzeiro,Vinicius Wilian D
(Sat Sep 01 2018 - 05:41:44 PDT)
[AMBER] Regarding error in MCPB.py
dhaval patel
(Sun Sep 02 2018 - 02:18:23 PDT)
Re: [AMBER] Regarding error in MCPB.py
Pengfei Li
(Tue Sep 04 2018 - 07:12:38 PDT)
[AMBER] Help in COM pulling
M RCC
(Sun Sep 02 2018 - 09:25:52 PDT)
[AMBER] Subtracting the forces from harmonic restraints
Nikolay N. Kuzmich
(Mon Sep 03 2018 - 01:52:57 PDT)
Re: [AMBER] Parameters for non-standard residues
Anuja Ware
(Mon Sep 03 2018 - 04:10:19 PDT)
Re: [AMBER] Normal mode calculation on a truncated system
David A Case
(Mon Sep 03 2018 - 04:46:07 PDT)
Re: [AMBER] Distance HH TIP3P
David A Case
(Mon Sep 03 2018 - 04:47:40 PDT)
Re: [AMBER] cpptraj segmentation fault when using avgout in cluster
Charo del Genio
(Mon Sep 03 2018 - 07:07:27 PDT)
[AMBER] Format of cpptraj pairwise distance file when clustering
Charo del Genio
(Mon Sep 03 2018 - 07:18:02 PDT)
Re: [AMBER] Format of cpptraj pairwise distance file when clustering
Daniel Roe
(Mon Sep 03 2018 - 11:49:34 PDT)
Re: [AMBER] Format of cpptraj pairwise distance file when clustering
Charo del Genio
(Tue Sep 04 2018 - 01:00:48 PDT)
Re: [AMBER] Format of cpptraj pairwise distance file when clustering
Daniel Roe
(Tue Sep 04 2018 - 08:02:53 PDT)
Re: [AMBER] Format of cpptraj pairwise distance file when clustering
Daniel Roe
(Tue Sep 04 2018 - 12:26:16 PDT)
[AMBER] parameterizing the covalently bonded ligand
hosein geraili
(Mon Sep 03 2018 - 09:25:24 PDT)
[AMBER] Coordinate messed up after tleap set box
Simon Kit Sang Chu
(Mon Sep 03 2018 - 12:31:32 PDT)
Re: [AMBER] Coordinate messed up after tleap set box
David A Case
(Tue Sep 04 2018 - 05:28:36 PDT)
Re: [AMBER] Coordinate messed up after tleap set box
Simon Kit Sang Chu
(Tue Sep 04 2018 - 09:58:33 PDT)
Re: [AMBER] Coordinate messed up after tleap set box
David A Case
(Tue Sep 04 2018 - 10:37:20 PDT)
Re: [AMBER] Coordinate messed up after tleap set box
Simon Kit Sang Chu
(Tue Sep 04 2018 - 11:39:48 PDT)
[AMBER] Regarding output file in REMD
Rajarshi Roy
(Mon Sep 03 2018 - 21:47:10 PDT)
[AMBER] [david.case.rutgers.edu: Re: Coordinate messed up after tleap set box]
David A Case
(Tue Sep 04 2018 - 05:31:36 PDT)
Re: [AMBER] Need help regarding calculation of Coordination number from RDF Profile
Bharat Manna
(Tue Sep 04 2018 - 06:35:59 PDT)
[AMBER] Reg: antechamber net charge calculation -nc
Samdani A
(Tue Sep 04 2018 - 07:22:40 PDT)
Re: [AMBER] Reg: antechamber net charge calculation -nc
David A Case
(Tue Sep 04 2018 - 10:46:58 PDT)
[AMBER] GTX-2080 benchmarks
Piotr Fajer
(Tue Sep 04 2018 - 10:04:49 PDT)
Re: [AMBER] GTX-2080 benchmarks
David Cerutti
(Tue Sep 04 2018 - 10:24:06 PDT)
[AMBER] RMS is zero
Hadi Rahmaninejad
(Tue Sep 04 2018 - 13:34:23 PDT)
Re: [AMBER] RMS is zero
Stephan Schott
(Tue Sep 04 2018 - 13:58:04 PDT)
Re: [AMBER] RMS is zero
Hadi Rahmaninejad
(Tue Sep 04 2018 - 14:19:08 PDT)
[AMBER] Restraining forces for atoms
Nikolay N. Kuzmich
(Wed Sep 05 2018 - 01:06:12 PDT)
Re: [AMBER] Restraining forces for atoms
Bill Ross
(Wed Sep 05 2018 - 01:17:52 PDT)
Re: [AMBER] Restraining forces for atoms
Nikolay N. Kuzmich
(Thu Sep 06 2018 - 05:46:42 PDT)
Re: [AMBER] Restraining forces for atoms
Bill Ross
(Thu Sep 06 2018 - 09:07:23 PDT)
[AMBER] Fwd: Problem with energy minimization sander.MPI
maryam azimzadehirani
(Wed Sep 05 2018 - 01:54:14 PDT)
Re: [AMBER] Fwd: Problem with energy minimization sander.MPI
Bill Ross
(Wed Sep 05 2018 - 02:03:25 PDT)
Re: [AMBER] Fwd: Problem with energy minimization sander.MPI
maryam azimzadehirani
(Wed Sep 05 2018 - 02:34:17 PDT)
Re: [AMBER] Fwd: Problem with energy minimization sander.MPI
David A Case
(Wed Sep 05 2018 - 05:10:03 PDT)
Re: [AMBER] Fwd: Problem with energy minimization sander.MPI
maryam azimzadehirani
(Wed Sep 05 2018 - 07:03:20 PDT)
[AMBER] covalently bonded ligand
hosein geraili
(Wed Sep 05 2018 - 05:40:54 PDT)
Re: [AMBER] covalently bonded ligand
Pengfei Li
(Sat Sep 08 2018 - 11:30:14 PDT)
[AMBER] MCPB.py error (not reading chk file)
Sushi Shilpa
(Thu Sep 06 2018 - 01:58:22 PDT)
Re: [AMBER] MCPB.py error (not reading chk file)
Pengfei Li
(Sat Sep 08 2018 - 11:38:13 PDT)
[AMBER] Couldn't find VdW parameters
Sushi Shilpa
(Thu Sep 06 2018 - 05:20:02 PDT)
Re: [AMBER] Couldn't find VdW parameters
Jason Swails
(Thu Sep 06 2018 - 05:56:23 PDT)
Re: [AMBER] Couldn't find VdW parameters
Sushi Shilpa
(Fri Sep 07 2018 - 01:51:10 PDT)
[AMBER] Energy uints in mden file and mdout_analyzer.py
Meng Wu
(Thu Sep 06 2018 - 06:17:41 PDT)
Re: [AMBER] Energy uints in mden file and mdout_analyzer.py
David A Case
(Thu Sep 06 2018 - 11:59:39 PDT)
Re: [AMBER] Energy uints in mden file and mdout_analyzer.py
Meng Wu
(Thu Sep 06 2018 - 19:14:59 PDT)
Re: [AMBER] Energy uints in mden file and mdout_analyzer.py
Meng Wu
(Fri Sep 07 2018 - 20:42:52 PDT)
[AMBER] parmed pdb to crd
Neha Gandhi
(Fri Sep 07 2018 - 02:04:34 PDT)
Re: [AMBER] parmed pdb to crd
Jason Swails
(Fri Sep 07 2018 - 20:09:32 PDT)
[AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster
Markowska
(Fri Sep 07 2018 - 10:37:06 PDT)
Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster
David Cerutti
(Fri Sep 07 2018 - 10:46:41 PDT)
Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster
Markowska
(Fri Sep 07 2018 - 11:17:42 PDT)
Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster
David A Case
(Mon Sep 10 2018 - 08:20:55 PDT)
Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster
Ryan Novosielski
(Mon Sep 10 2018 - 13:33:09 PDT)
Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster
Ross Walker
(Mon Sep 10 2018 - 15:12:49 PDT)
[AMBER] Leap: Nuleotides addition
Aravind Ravichandran
(Sat Sep 08 2018 - 04:32:36 PDT)
Re: [AMBER] Leap: Nuleotides addition
David A Case
(Sat Sep 08 2018 - 07:31:39 PDT)
Re: [AMBER] metalParm2.xml or metalParm.xml
Pengfei Li
(Sat Sep 08 2018 - 11:46:38 PDT)
Re: [AMBER] Arsenous acid (H3AsO3) parameterization
Pengfei Li
(Sat Sep 08 2018 - 12:10:41 PDT)
Re: [AMBER] Au+++ ion parameter
Pengfei Li
(Sat Sep 08 2018 - 12:18:52 PDT)
Re: [AMBER] Au+++ ion parameter
Pengfei Li
(Sat Sep 08 2018 - 12:49:12 PDT)
[AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL
龚乾坤
(Tue Sep 11 2018 - 05:26:36 PDT)
Re: [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL
David A Case
(Tue Sep 11 2018 - 09:11:25 PDT)
Re: [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL
龚乾坤
(Tue Sep 11 2018 - 18:06:48 PDT)
Re: [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL
龚乾坤
(Tue Sep 11 2018 - 23:59:41 PDT)
[AMBER] RMS rotate about z-axis only
Wesley Michael Botello-Smith
(Tue Sep 11 2018 - 13:02:49 PDT)
Re: [AMBER] RMS rotate about z-axis only
Hai Nguyen
(Fri Sep 14 2018 - 08:07:01 PDT)
Re: [AMBER] RMS rotate about z-axis only
Daniel Roe
(Thu Sep 20 2018 - 08:25:03 PDT)
[AMBER] Question about configure Ambertool18 on Mac
tang.xiaping.outlook.com
(Tue Sep 11 2018 - 22:35:25 PDT)
Re: [AMBER] Question about configure Ambertool18 on Mac
Bill Ross
(Tue Sep 11 2018 - 22:46:11 PDT)
Re: [AMBER] Question about configure Ambertool18 on Mac
tang.xiaping.outlook.com
(Wed Sep 12 2018 - 00:29:08 PDT)
Re: [AMBER] Question about configure Ambertool18 on Mac
Bill Ross
(Wed Sep 12 2018 - 00:38:43 PDT)
Re: [AMBER] Question about configure Ambertool18 on Mac
tang.xiaping.outlook.com
(Wed Sep 12 2018 - 00:50:49 PDT)
Re: [AMBER] Question about configure Ambertool18 on Mac
Bill Ross
(Wed Sep 12 2018 - 01:06:26 PDT)
Re: [AMBER] Question about configure Ambertool18 on Mac
David A Case
(Wed Sep 12 2018 - 05:08:42 PDT)
[AMBER] Query for umbrella sampling
Saikat Pal
(Wed Sep 12 2018 - 00:09:01 PDT)
[AMBER] Query for umbrella sampling
Saikat Pal
(Wed Sep 12 2018 - 13:36:57 PDT)
Re: [AMBER] Query for umbrella sampling
Bill Ross
(Wed Sep 12 2018 - 13:41:32 PDT)
[AMBER] Residue mutation and side chains
Benjamin Clausen
(Wed Sep 12 2018 - 04:01:50 PDT)
Re: [AMBER] Residue mutation and side chains
Carlos Simmerling
(Wed Sep 12 2018 - 09:25:16 PDT)
Re: [AMBER] Residue mutation and side chains
Benjamin Clausen
(Thu Sep 13 2018 - 00:15:57 PDT)
Re: [AMBER] Residue mutation and side chains
Bill Ross
(Thu Sep 13 2018 - 00:23:03 PDT)
Re: [AMBER] Residue mutation and side chains
Carlos Simmerling
(Thu Sep 13 2018 - 08:41:48 PDT)
[AMBER] difference of distances using cpptraj in free energy plot
Nisha Amarnath Jonniya
(Wed Sep 12 2018 - 05:07:10 PDT)
Re: [AMBER] difference of distances using cpptraj in free energy plot
Daniel Roe
(Wed Sep 12 2018 - 10:55:23 PDT)
Re: [AMBER] difference of distances using cpptraj in free energy plot
Nisha Amarnath Jonniya
(Thu Sep 13 2018 - 00:34:53 PDT)
[AMBER] CPPTRAJ: extracting the restraining forces
Nikolay N. Kuzmich
(Wed Sep 12 2018 - 06:02:47 PDT)
Re: [AMBER] CPPTRAJ: extracting the restraining forces
Daniel Roe
(Thu Sep 20 2018 - 08:45:32 PDT)
[AMBER] A confusion about the binding energy calculated by pbsa with implicit membrane model
高振梅
(Wed Sep 12 2018 - 06:15:50 PDT)
Re: [AMBER] A confusion about the binding energy calculated by pbsa with implicit membrane model
Ray Luo
(Wed Sep 12 2018 - 10:35:32 PDT)
[AMBER] Amber constraint SMD
李耀
(Wed Sep 12 2018 - 08:17:30 PDT)
[AMBER] more about gfortran8.2 and clang9.1: no cpptraj problems here
David A Case
(Wed Sep 12 2018 - 13:28:34 PDT)
Re: [AMBER] more about gfortran8.2 and clang9.1: no cpptraj problems here
Bill Ross
(Wed Sep 12 2018 - 13:35:08 PDT)
Re: [AMBER] more about gfortran8.2 and clang9.1: no cpptraj problems here
Bill Ross
(Wed Sep 12 2018 - 13:38:55 PDT)
[AMBER] H-bond between the substrate molecule and protein in the MD traj
Meng Wu
(Wed Sep 12 2018 - 18:30:49 PDT)
Re: [AMBER] H-bond between the substrate molecule and protein in the MD traj
Gustaf Olsson
(Wed Sep 12 2018 - 23:16:14 PDT)
Re: [AMBER] H-bond between the substrate molecule and protein in the MD traj
Daniel Roe
(Thu Sep 13 2018 - 06:09:18 PDT)
[AMBER] Some questions about mmpbsa.py
龚乾坤
(Thu Sep 13 2018 - 00:01:12 PDT)
Re: [AMBER] Some questions about mmpbsa.py
David A Case
(Thu Sep 13 2018 - 04:32:04 PDT)
[AMBER] Compression of CDF coordinate files to gzip AMBER18.
DHEERAJ CHITARA
(Thu Sep 13 2018 - 01:12:44 PDT)
Re: [AMBER] Compression of CDF coordinate files to gzip AMBER18.
David A Case
(Thu Sep 13 2018 - 04:39:00 PDT)
[AMBER] Distance based energy calculation
MOHD HOMAIDUR RAHMAN
(Thu Sep 13 2018 - 06:45:52 PDT)
[AMBER] Fwd: Distance based energy calculation
MOHD HOMAIDUR RAHMAN
(Tue Sep 18 2018 - 23:32:03 PDT)
Re: [AMBER] Distance based energy calculation
Daniel Roe
(Thu Sep 20 2018 - 08:13:41 PDT)
[AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ?
Bharat Manna
(Thu Sep 13 2018 - 11:48:48 PDT)
Re: [AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ?
Matias Machado
(Sun Sep 16 2018 - 07:50:47 PDT)
Re: [AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ?
Bharat Manna
(Thu Sep 20 2018 - 20:30:19 PDT)
[AMBER] a error about MMPBSA.PY
龚乾坤
(Thu Sep 13 2018 - 17:29:07 PDT)
Re: [AMBER] a error about MMPBSA.PY
David A Case
(Fri Sep 14 2018 - 05:40:24 PDT)
[AMBER] Query regarding the number of cores for running sander.MPI
Leena Aggarwal
(Fri Sep 14 2018 - 01:25:42 PDT)
Re: [AMBER] Query regarding the number of cores for running sander.MPI
Stephan Schott
(Fri Sep 14 2018 - 01:43:18 PDT)
[AMBER] Question about Amber.
Asier Zorrilla
(Fri Sep 14 2018 - 05:08:37 PDT)
Re: [AMBER] Question about Amber.
Carlos Simmerling
(Fri Sep 14 2018 - 05:17:15 PDT)
Re: [AMBER] Question about Amber.
Adrian Roitberg
(Fri Sep 14 2018 - 05:39:51 PDT)
Re: [AMBER] Question about Amber.
David A Case
(Fri Sep 14 2018 - 05:53:49 PDT)
Re: [AMBER] Question about Amber.
Asier Zorrilla
(Mon Sep 17 2018 - 01:25:00 PDT)
Re: [AMBER] Question about Amber.
Bill Ross
(Mon Sep 17 2018 - 01:40:01 PDT)
Re: [AMBER] Question about Amber.
Asier Zorrilla
(Fri Sep 21 2018 - 05:00:42 PDT)
[AMBER] A confusion about the binding energy calculated by pbsa with implicit membrane model
高振梅
(Fri Sep 14 2018 - 06:25:56 PDT)
[AMBER] Error in umbrella sampling
Saikat Pal
(Fri Sep 14 2018 - 07:26:14 PDT)
Re: [AMBER] Error in umbrella sampling
Bill Ross
(Fri Sep 14 2018 - 09:47:11 PDT)
Re: [AMBER] Error in umbrella sampling
Saikat Pal
(Mon Sep 17 2018 - 08:50:53 PDT)
Re: [AMBER] Error in umbrella sampling
David A Case
(Mon Sep 17 2018 - 10:10:20 PDT)
Re: [AMBER] Error in umbrella sampling
Saikat Pal
(Mon Sep 17 2018 - 10:23:41 PDT)
Re: [AMBER] Error in umbrella sampling
Saikat Pal
(Tue Sep 18 2018 - 07:30:02 PDT)
[AMBER] Protein "jumping" during SMD run
Cory Ayres
(Fri Sep 14 2018 - 08:13:16 PDT)
Re: [AMBER] Protein "jumping" during SMD run
Carlos Simmerling
(Fri Sep 14 2018 - 13:32:53 PDT)
[AMBER] rdf in one dimmension
Hadi Rahmaninejad
(Fri Sep 14 2018 - 13:29:25 PDT)
Re: [AMBER] rdf in one dimmension
Tom Kurtzman
(Fri Sep 14 2018 - 18:36:17 PDT)
Re: [AMBER] rdf in one dimmension
Tom Kurtzman
(Fri Sep 14 2018 - 18:48:20 PDT)
Re: [AMBER] rdf in one dimmension
Hadi Rahmaninejad
(Sun Sep 16 2018 - 17:32:30 PDT)
Re: [AMBER] rdf in one dimmension
Daniel Roe
(Mon Sep 17 2018 - 04:22:57 PDT)
Re: [AMBER] rdf in one dimmension
Tom Kurtzman
(Mon Sep 17 2018 - 19:49:35 PDT)
[AMBER] why not free QM software？
Albert
(Sat Sep 15 2018 - 07:42:01 PDT)
Re: [AMBER] why not free QM software？
Charles-Alexandre Mattelaer
(Sat Sep 15 2018 - 07:47:41 PDT)
Re: [AMBER] why not free QM software？
Gustavo Seabra
(Sun Sep 16 2018 - 11:49:33 PDT)
Re: [AMBER] why not free QM software？
Albert
(Sun Sep 16 2018 - 12:23:19 PDT)
Re: [AMBER] why not free QM software？
Gustavo Seabra
(Sun Sep 16 2018 - 12:33:38 PDT)
[AMBER] Newbie question about installing AmberTool18 in Linux (VirtualBox)
leifepeterson.sbcglobal.net
(Sat Sep 15 2018 - 09:28:16 PDT)
Re: [AMBER] Newbie question about installing AmberTool18 in Linux (VirtualBox)
Hai Nguyen
(Sun Sep 16 2018 - 15:00:46 PDT)
[AMBER] Installing fortran in Ubuntu-64 for Sander
leifepeterson.sbcglobal.net
(Sat Sep 15 2018 - 13:03:50 PDT)
Re: [AMBER] Installing fortran in Ubuntu-64 for Sander
Dwight McGee
(Sat Sep 15 2018 - 17:35:31 PDT)
[AMBER] RESOLVED: Installing fortran in Ubuntu-64 for Sander
leifepeterson.sbcglobal.net
(Sat Sep 15 2018 - 19:15:25 PDT)
[AMBER] Sander 01_Min.out error
leifepeterson.sbcglobal.net
(Sat Sep 15 2018 - 19:23:44 PDT)
[AMBER] RESOLVED: peek_ewald_inpcrd: Box info not found in inpcrd
leifepeterson.sbcglobal.net
(Sat Sep 15 2018 - 20:24:35 PDT)
Re: [AMBER] RESOLVED: peek_ewald_inpcrd: Box info not found in inpcrd
Matias Machado
(Sun Sep 16 2018 - 08:35:10 PDT)
[AMBER] unwrap problem in the liquid water dynamics trajectory analysis
jinfeng liu
(Sat Sep 15 2018 - 22:43:13 PDT)
Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis
Matias Machado
(Sun Sep 16 2018 - 06:52:54 PDT)
Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis
Matias Machado
(Sun Sep 16 2018 - 07:04:09 PDT)
Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis
jinfeng liu
(Sun Sep 16 2018 - 18:21:31 PDT)
Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis
David A Case
(Sun Sep 16 2018 - 17:59:18 PDT)
Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis
jinfeng liu
(Sun Sep 16 2018 - 18:47:44 PDT)
Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis
Daniel Roe
(Mon Sep 17 2018 - 04:21:51 PDT)
[AMBER] Clustering_distance_metric_option_general_rule
Antonio Amber Carlesso
(Sun Sep 16 2018 - 01:26:25 PDT)
Re: [AMBER] Clustering_distance_metric_option_general_rule
Daniel Roe
(Thu Sep 20 2018 - 08:21:26 PDT)
Re: [AMBER] Clustering_distance_metric_option_general_rule
Christina Bergonzo
(Thu Sep 20 2018 - 08:47:55 PDT)
Re: [AMBER] Clustering_distance_metric_option_general_rule
Antonio Amber Carlesso
(Thu Sep 27 2018 - 14:07:15 PDT)
[AMBER] Adding 12_6_4 LJ parameters in prmtop file
Deepika Sardana
(Sun Sep 16 2018 - 09:33:18 PDT)
Re: [AMBER] Adding 12_6_4 LJ parameters in prmtop file
Pengfei Li
(Sat Sep 22 2018 - 07:41:42 PDT)
Re: [AMBER] Adding 12_6_4 LJ parameters in prmtop file
Pengfei Li
(Sat Sep 22 2018 - 07:42:55 PDT)
[AMBER] AMBER Alanine tutorial (different outputs from AMBER15 and AMBER18)
leifepeterson.sbcglobal.net
(Sun Sep 16 2018 - 12:30:24 PDT)
Re: [AMBER] AMBER Alanine tutorial (different outputs from AMBER15 and AMBER18)
Matias Machado
(Sun Sep 16 2018 - 13:18:29 PDT)
[AMBER] Options for nonpolar solvation free energy calculation with mm_pbsa.pl
龚乾坤
(Sun Sep 16 2018 - 19:50:56 PDT)
Re: [AMBER] Options for nonpolar solvation free energy calculation with mm_pbsa.pl
David A Case
(Mon Sep 24 2018 - 04:32:26 PDT)
[AMBER] RESOLVED: AMBER Alanine tutorial (need to replace .mdcrd with .nc)
leifepeterson.sbcglobal.net
(Mon Sep 17 2018 - 06:36:34 PDT)
[AMBER] test errors of amber18
Lei Zhao
(Mon Sep 17 2018 - 06:41:34 PDT)
Re: [AMBER] test errors of amber18
David Case
(Thu Sep 27 2018 - 04:51:59 PDT)
[AMBER] pbsa:cannot match namelist object name mprob
高振梅
(Mon Sep 17 2018 - 07:00:46 PDT)
Re: [AMBER] pbsa:cannot match namelist object name mprob
Ray Luo
(Mon Sep 17 2018 - 10:15:21 PDT)
[AMBER] Contact Map
Sourav Purohit
(Mon Sep 17 2018 - 15:59:06 PDT)
Re: [AMBER] Contact Map
Daniel Roe
(Thu Sep 20 2018 - 06:00:58 PDT)
Re: [AMBER] Contact Map
Sourav Purohit
(Thu Sep 20 2018 - 11:24:01 PDT)
Re: [AMBER] Contact Map
Daniel Roe
(Mon Sep 24 2018 - 08:46:58 PDT)
Re: [AMBER] Contact Map
Daniel Roe
(Mon Sep 24 2018 - 08:48:33 PDT)
[AMBER] Amber16 cuda compiling error
senal dinuka
(Mon Sep 17 2018 - 20:43:19 PDT)
Re: [AMBER] Amber16 cuda compiling error
David Cerutti
(Mon Sep 17 2018 - 20:47:11 PDT)
Re: [AMBER] Amber16 cuda compiling error
senal dinuka
(Mon Sep 17 2018 - 21:13:58 PDT)
Re: [AMBER] Amber16 cuda compiling error
David Cerutti
(Mon Sep 17 2018 - 21:33:00 PDT)
Re: [AMBER] Amber16 cuda compiling error
David Case
(Tue Sep 18 2018 - 06:18:54 PDT)
[AMBER] Amber Installation Error
Yuthika Dholey
(Mon Sep 17 2018 - 22:46:02 PDT)
Re: [AMBER] Amber Installation Error
David Case
(Tue Sep 18 2018 - 06:21:49 PDT)
[AMBER] Regarding nastruct command in cpptraj
Rajarshi Roy
(Tue Sep 18 2018 - 10:39:41 PDT)
Re: [AMBER] Regarding nastruct command in cpptraj
Daniel Roe
(Thu Sep 20 2018 - 07:40:39 PDT)
Re: [AMBER] Regarding nastruct command in cpptraj
Rajarshi Roy
(Fri Sep 21 2018 - 00:35:42 PDT)
Re: [AMBER] Regarding nastruct command in cpptraj
Daniel Roe
(Fri Sep 21 2018 - 09:09:47 PDT)
Re: [AMBER] Regarding nastruct command in cpptraj
Rajarshi Roy
(Fri Sep 21 2018 - 22:01:54 PDT)
[AMBER] atomic fluctuation vs residue
Avirup Ghosh
(Tue Sep 18 2018 - 19:26:19 PDT)
Re: [AMBER] atomic fluctuation vs residue
Daniel Roe
(Thu Sep 20 2018 - 07:42:08 PDT)
[AMBER] Problem in testing the Zinc enzyme example using MCPB.py
Alex Schwartz
(Tue Sep 18 2018 - 20:55:07 PDT)
Re: [AMBER] Problem in testing the Zinc enzyme example using MCPB.py
Pengfei Li
(Sat Sep 22 2018 - 07:31:16 PDT)
[AMBER] Unknown keyword
Sushi Shilpa
(Wed Sep 19 2018 - 02:55:54 PDT)
Re: [AMBER] Unknown keyword
Bill Ross
(Wed Sep 19 2018 - 03:04:48 PDT)
[AMBER] Problem with stripping with a condition
Hadi Rahmaninejad
(Wed Sep 19 2018 - 08:56:43 PDT)
Re: [AMBER] Problem with stripping with a condition
Daniel Roe
(Thu Sep 20 2018 - 05:49:44 PDT)
[AMBER] Running GIST calculation in parallel
M RCC
(Thu Sep 20 2018 - 02:57:44 PDT)
Re: [AMBER] Running GIST calculation in parallel
Daniel Roe
(Thu Sep 20 2018 - 08:37:37 PDT)
Re: [AMBER] Running GIST calculation in parallel
M RCC
(Fri Sep 21 2018 - 07:53:03 PDT)
Re: [AMBER] Running GIST calculation in parallel
Daniel Roe
(Fri Sep 21 2018 - 10:18:41 PDT)
Re: [AMBER] Running GIST calculation in parallel
Matias Machado
(Fri Sep 21 2018 - 11:16:07 PDT)
Re: [AMBER] Running GIST calculation in parallel
Tom Kurtzman
(Fri Sep 21 2018 - 15:35:32 PDT)
Re: [AMBER] Running GIST calculation in parallel
Matias Machado
(Sun Sep 23 2018 - 06:08:22 PDT)
[AMBER] Amber on GPU
emanuele falbo
(Thu Sep 20 2018 - 03:13:40 PDT)
Re: [AMBER] Amber on GPU
David A Case
(Thu Sep 20 2018 - 04:14:54 PDT)
Re: [AMBER] Amber on GPU
emanuele falbo
(Thu Sep 20 2018 - 04:23:04 PDT)
Re: [AMBER] QM/MM Thermodynamic Integration
emanuele falbo
(Thu Sep 20 2018 - 04:29:22 PDT)
Re: [AMBER] QM/MM Thermodynamic Integration
Goetz, Andreas
(Thu Sep 20 2018 - 09:50:57 PDT)
[AMBER] Temperature RMS, ntslim limit
Nikolay N. Kuzmich
(Thu Sep 20 2018 - 05:29:24 PDT)
Re: [AMBER] Temperature RMS, ntslim limit
Matias Machado
(Thu Sep 20 2018 - 07:48:35 PDT)
[AMBER] Seeking clarification regarding Calculation of Linear Interaction Energy (lie)
Bharat Manna
(Thu Sep 20 2018 - 20:25:51 PDT)
Re: [AMBER] AMBER ntslim limit
Nikolay N. Kuzmich
(Fri Sep 21 2018 - 02:34:30 PDT)
Re: [AMBER] AMBER ntslim limit
Bill Ross
(Fri Sep 21 2018 - 02:46:10 PDT)
Re: [AMBER] AMBER ntslim limit
Matias Machado
(Fri Sep 21 2018 - 05:06:16 PDT)
[AMBER] cuda 10 support
Waqas Takkar
(Fri Sep 21 2018 - 03:42:04 PDT)
Re: [AMBER] cuda 10 support
David Cerutti
(Fri Sep 21 2018 - 08:41:57 PDT)
[AMBER] Query on 2DRMSD
Saikat Pal
(Fri Sep 21 2018 - 05:03:09 PDT)
Re: [AMBER] Query on 2DRMSD
Thomas Cheatham
(Fri Sep 21 2018 - 17:09:41 PDT)
[AMBER] setting of different concentration of Nacl
Nisha Amarnath Jonniya
(Fri Sep 21 2018 - 05:40:52 PDT)
Re: [AMBER] setting of different concentration of Nacl
Matias Machado
(Fri Sep 21 2018 - 07:10:30 PDT)
Re: [AMBER] setting of different concentration of Nacl
Stephan Schott
(Fri Sep 21 2018 - 07:49:30 PDT)
Re: [AMBER] setting of different concentration of Nacl
Matias Machado
(Fri Sep 21 2018 - 07:58:16 PDT)
Re: [AMBER] setting of different concentration of Nacl
Stephan Schott
(Fri Sep 21 2018 - 08:13:31 PDT)
[AMBER] Critical Isoform selectivity in MD
M RCC
(Sun Sep 23 2018 - 23:15:49 PDT)
Re: [AMBER] Critical Isoform selectivity in MD
David Case
(Thu Sep 27 2018 - 04:46:52 PDT)
[AMBER] Error while creating topology file(HMassRepartition) in parmed
Aravind Ravichandran
(Mon Sep 24 2018 - 03:39:09 PDT)
Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed
David A Case
(Mon Sep 24 2018 - 04:39:26 PDT)
Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed
David A Case
(Mon Sep 24 2018 - 04:42:28 PDT)
Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed
David Case
(Mon Sep 24 2018 - 16:11:47 PDT)
[AMBER] SMD free energy inferred from work
Ruth Helena Tichauer
(Mon Sep 24 2018 - 06:46:42 PDT)
Re: [AMBER] SMD free energy inferred from work
Feng Pan
(Mon Sep 24 2018 - 08:38:09 PDT)
Re: [AMBER] SMD free energy inferred from work
Ruth Helena Tichauer
(Mon Sep 24 2018 - 13:16:10 PDT)
[AMBER] nVidia Webinar: Achievable Free Energy Calculations through GPU-Accelerated AMBER
accuratefreeenergy.gmail.com
(Mon Sep 24 2018 - 10:28:14 PDT)
Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16
Paul Westphälinger
(Tue Sep 25 2018 - 03:43:55 PDT)
Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16
James Kress
(Tue Sep 25 2018 - 09:49:54 PDT)
Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16
Paul Westphälinger
(Wed Sep 26 2018 - 04:10:04 PDT)
[AMBER] PBC error. Amber force field in NAMD
M RCC
(Tue Sep 25 2018 - 04:34:54 PDT)
Re: [AMBER] PBC error. Amber force field in NAMD
Eric Lang
(Tue Sep 25 2018 - 06:34:28 PDT)
[AMBER] Calculating residence times with cpptraj
Stefan Ivanov
(Tue Sep 25 2018 - 21:52:54 PDT)
Re: [AMBER] Calculating residence times with cpptraj
Daniel Roe
(Wed Sep 26 2018 - 12:08:57 PDT)
[AMBER] Reducing memory usage in lifetime analyses
Gustaf Olsson
(Tue Sep 25 2018 - 23:15:29 PDT)
Re: [AMBER] Reducing memory usage in lifetime analyses
Daniel Roe
(Wed Sep 26 2018 - 12:14:10 PDT)
Re: [AMBER] Reducing memory usage in lifetime analyses
Gustaf Olsson
(Fri Sep 28 2018 - 00:20:42 PDT)
[AMBER] Problem with antechamber/acdoctor
Sarah Fegan - UKRI STFC
(Wed Sep 26 2018 - 03:15:11 PDT)
Re: [AMBER] Re-scaling masses and kinetic energy in TI calculations
David Case
(Thu Sep 27 2018 - 04:42:42 PDT)
Re: [AMBER] Re-scaling masses and kinetic energy in TI calculations
Tom Kurtzman
(Thu Sep 27 2018 - 05:29:51 PDT)
[AMBER] Counter Ions in X-Ray structure.
Keiran Corbett
(Thu Sep 27 2018 - 04:55:35 PDT)
Re: [AMBER] Counter Ions in X-Ray structure.
David Case
(Thu Sep 27 2018 - 05:53:16 PDT)
Re: [AMBER] Counter Ions in X-Ray structure.
Keiran Corbett
(Thu Sep 27 2018 - 07:08:27 PDT)
Re: [AMBER] Counter Ions in X-Ray structure.
Keiran Corbett
(Thu Sep 27 2018 - 07:38:52 PDT)
Re: [AMBER] Counter Ions in X-Ray structure.
Matias Machado
(Thu Sep 27 2018 - 09:24:24 PDT)
Re: [AMBER] Counter Ions in X-Ray structure.
Matias Machado
(Thu Sep 27 2018 - 10:25:17 PDT)
Re: [AMBER] Counter Ions in X-Ray structure.
David Case
(Thu Sep 27 2018 - 13:29:38 PDT)
[AMBER] annoying elapsed time in mdout of amber18
Song-Ho Chong
(Thu Sep 27 2018 - 05:57:00 PDT)
Re: [AMBER] annoying elapsed time in mdout of amber18
David Case
(Thu Sep 27 2018 - 13:36:36 PDT)
Re: [AMBER] annoying elapsed time in mdout of amber18
Song-Ho Chong
(Thu Sep 27 2018 - 20:38:57 PDT)
Re: [AMBER] annoying elapsed time in mdout of amber18
Song-Ho Chong
(Fri Sep 28 2018 - 00:15:24 PDT)
Re: [AMBER] annoying elapsed time in mdout of amber18
James Kress
(Fri Sep 28 2018 - 09:18:53 PDT)
Re: [AMBER] annoying elapsed time in mdout of amber18
Song-Ho Chong
(Fri Sep 28 2018 - 09:23:26 PDT)
[AMBER] Umbrella sampling scripts
emanuele falbo
(Thu Sep 27 2018 - 06:33:59 PDT)
Re: [AMBER] Umbrella sampling scripts
Marcos Serrou do Amaral
(Thu Sep 27 2018 - 06:51:27 PDT)
Re: [AMBER] Umbrella sampling scripts
emanuele falbo
(Thu Sep 27 2018 - 06:56:58 PDT)
Re: [AMBER] Umbrella sampling scripts
emanuele falbo
(Thu Sep 27 2018 - 07:14:28 PDT)
Re: [AMBER] Umbrella sampling scripts
Marcos Serrou do Amaral
(Thu Sep 27 2018 - 07:54:03 PDT)
Re: [AMBER] Umbrella sampling scripts
emanuele falbo
(Thu Sep 27 2018 - 11:43:50 PDT)
[AMBER] NVIDIA GPU RTX 2080 / RTX 2080 Ti
Alain Chaumont
(Thu Sep 27 2018 - 09:55:11 PDT)
Re: [AMBER] NVIDIA GPU RTX 2080 / RTX 2080 Ti
David Cerutti
(Thu Sep 27 2018 - 10:18:50 PDT)
[AMBER] Problems with MPI compilation gb_force.F90
Ruben Ramos Horta
(Fri Sep 28 2018 - 01:05:10 PDT)
Re: [AMBER] Problems with MPI compilation gb_force.F90
David Case
(Fri Sep 28 2018 - 04:28:31 PDT)
Re: [AMBER] Problems with MPI compilation gb_force.F90
James Kress
(Fri Sep 28 2018 - 09:16:49 PDT)
[AMBER] How to computing peptide partial charges with antechamber?
yulongsun.nwpu.edu.cn
(Sat Sep 29 2018 - 06:59:53 PDT)
Re: [AMBER] How to computing peptide partial charges with antechamber?
David Case
(Sat Sep 29 2018 - 10:54:01 PDT)
Last message date
:
Sat Sep 29 2018 - 11:00:03 PDT
Archived on
: Wed Oct 30 2024 - 05:55:43 PDT
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