Amber Archive Apr 2019 by subject
310 messages
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Starting
Sun Mar 31 2019 - 18:00:02 PDT,
Ending
Tue Apr 30 2019 - 13:00:03 PDT
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[AMBER] "Problem installing Miniconda"
Seibold, Steve Allan
(Thu Apr 18 2019 - 11:44:39 PDT)
Hai Nguyen
(Thu Apr 18 2019 - 11:00:05 PDT)
David A Case
(Thu Apr 18 2019 - 10:55:27 PDT)
Hai Nguyen
(Thu Apr 18 2019 - 08:57:55 PDT)
Seibold, Steve Allan
(Thu Apr 18 2019 - 08:43:30 PDT)
[AMBER] 2 job positions InterX Inc. Molecular Simulation and Molecular ForceField Scientists
Ganesh Kamath
(Sat Apr 06 2019 - 08:00:24 PDT)
Ganesh Kamath
(Fri Apr 05 2019 - 12:58:51 PDT)
[AMBER] [rok.ucsd.edu: AT19 cpptraj MPI build issue (Linux, x86_64, gnu)]
David A Case
(Tue Apr 30 2019 - 12:55:23 PDT)
[AMBER] A-DNA
Charu Sharma (JRF)
(Tue Apr 23 2019 - 11:51:09 PDT)
David Case
(Tue Apr 23 2019 - 05:13:52 PDT)
Charu Sharma (JRF)
(Mon Apr 22 2019 - 22:17:26 PDT)
[AMBER] AMBER - Heating MD Systems
An Ta
(Thu Apr 18 2019 - 10:58:58 PDT)
Carlos Simmerling
(Thu Apr 18 2019 - 08:43:54 PDT)
Lin Song
(Thu Apr 18 2019 - 08:38:30 PDT)
An Ta
(Thu Apr 18 2019 - 06:23:32 PDT)
Carlos Simmerling
(Thu Apr 18 2019 - 06:03:41 PDT)
An Ta
(Thu Apr 18 2019 - 05:48:37 PDT)
[AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang
Gustaf Olsson
(Sun Apr 28 2019 - 14:12:38 PDT)
David Case
(Sun Apr 28 2019 - 09:49:13 PDT)
Gustaf Olsson
(Sat Apr 27 2019 - 11:25:03 PDT)
Hai Nguyen
(Sat Apr 27 2019 - 09:36:49 PDT)
Gustaf Olsson
(Sat Apr 27 2019 - 05:58:27 PDT)
[AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - GCC8.3
Gustaf Olsson
(Sat Apr 27 2019 - 11:44:00 PDT)
[AMBER] Antechamber question
David Poole
(Thu Apr 25 2019 - 16:03:37 PDT)
[AMBER] Any help on how to implement it in cpptraj?
Daniel Roe
(Tue Apr 30 2019 - 06:43:21 PDT)
Debarati DasGupta
(Fri Apr 26 2019 - 09:25:11 PDT)
[AMBER] Atoms per processor
David A Case
(Mon Apr 15 2019 - 07:37:15 PDT)
Charo del Genio
(Mon Apr 15 2019 - 04:36:10 PDT)
[AMBER] Box with a “separator”
Alessandro Mariani
(Tue Apr 02 2019 - 02:59:01 PDT)
[AMBER] Calculate zero point energy for a protein (no ligand) system
MOHD HOMAIDUR RAHMAN
(Tue Apr 09 2019 - 11:49:17 PDT)
Akshay Prabhakant
(Tue Apr 09 2019 - 05:46:42 PDT)
Carlos Simmerling
(Tue Apr 09 2019 - 05:36:05 PDT)
Akshay Prabhakant
(Tue Apr 09 2019 - 05:32:19 PDT)
Robert Molt
(Tue Apr 09 2019 - 05:26:43 PDT)
Carlos Simmerling
(Tue Apr 09 2019 - 04:47:57 PDT)
Akshay Prabhakant
(Tue Apr 09 2019 - 04:42:58 PDT)
[AMBER] Can Amber constant pH run with CHARMM force field?
Jason Swails
(Sun Apr 07 2019 - 17:19:37 PDT)
Chen Yifan
(Fri Apr 05 2019 - 19:12:56 PDT)
Cruzeiro,Vinicius Wilian D
(Fri Apr 05 2019 - 16:15:16 PDT)
Feng, Zimin
(Fri Apr 05 2019 - 13:56:57 PDT)
Chen Yifan
(Fri Apr 05 2019 - 11:51:35 PDT)
[AMBER] Capping RNA
David A Case
(Thu Apr 11 2019 - 07:03:46 PDT)
Mihaljevic-Juric Paula (Mme)
(Thu Apr 11 2019 - 02:56:08 PDT)
[AMBER] Change the trajectory format.
Daniel Roe
(Thu Apr 25 2019 - 04:54:18 PDT)
Thomas Cheatham
(Wed Apr 24 2019 - 23:15:14 PDT)
Parviz Seifpanahi Shabane
(Fri Apr 19 2019 - 12:12:39 PDT)
[AMBER] charge in constant redox cein file vs. prmtop file
Feng, Zimin
(Wed Apr 24 2019 - 11:10:41 PDT)
Cruzeiro,Vinicius Wilian D
(Wed Apr 24 2019 - 09:51:12 PDT)
Feng, Zimin
(Wed Apr 24 2019 - 09:14:30 PDT)
Cruzeiro,Vinicius Wilian D
(Tue Apr 23 2019 - 15:51:31 PDT)
Feng, Zimin
(Tue Apr 23 2019 - 15:03:24 PDT)
[AMBER] charged residue mutation free energy
Hosein Geraili Daronkola
(Fri Apr 12 2019 - 00:04:12 PDT)
[AMBER] COM Dihedral Restraint
Kellon Belfon
(Thu Apr 11 2019 - 09:34:45 PDT)
Kung, Ryan
(Thu Apr 11 2019 - 08:23:17 PDT)
[AMBER] Computing forces by trajectory post-processing with sander
Casalini Tommaso
(Wed Apr 24 2019 - 01:09:51 PDT)
Daniel Roe
(Tue Apr 23 2019 - 06:56:30 PDT)
Yuliana Bosken
(Mon Apr 22 2019 - 20:44:34 PDT)
Alen Ahmetovic
(Mon Apr 22 2019 - 16:50:40 PDT)
Casalini Tommaso
(Mon Apr 22 2019 - 12:54:10 PDT)
[AMBER] Confusion regarding ff14SB and ff99SBildn forcefields
David Cerutti
(Fri Apr 12 2019 - 00:36:01 PDT)
RITUPARNA ROY
(Fri Apr 12 2019 - 00:09:12 PDT)
[AMBER] constant-pressure equilibration with a water droplet
David A Case
(Mon Apr 29 2019 - 11:06:09 PDT)
Carlos Simmerling
(Mon Apr 29 2019 - 09:07:25 PDT)
Anthony Bogetti
(Mon Apr 29 2019 - 08:37:40 PDT)
[AMBER] CPPTRAJ gnu extension not working
anu chandra
(Tue Apr 30 2019 - 10:00:08 PDT)
[AMBER] Creating a water model from scratch
David Cerutti
(Mon Apr 08 2019 - 12:36:46 PDT)
Gustavo Seabra
(Mon Apr 08 2019 - 11:55:39 PDT)
[AMBER] cReAtInG PDB
David A Case
(Thu Apr 11 2019 - 07:06:11 PDT)
Boutheïna KERKENI
(Thu Apr 11 2019 - 03:13:20 PDT)
[AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed
Ross Walker
(Thu Apr 04 2019 - 07:36:32 PDT)
bjyx20090941
(Wed Apr 03 2019 - 20:21:49 PDT)
[AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol ( GeForce RTX 2080)
accuratefreeenergy.gmail.com
(Wed Apr 03 2019 - 07:36:36 PDT)
bjyx20090941
(Wed Apr 03 2019 - 07:24:23 PDT)
[AMBER] dihedral scanning with GAFF and GAFF2
Qasim Pars
(Fri Apr 26 2019 - 03:22:33 PDT)
[AMBER] Electrostatic interactions in LIE method
Debarati DasGupta
(Thu Apr 11 2019 - 10:57:19 PDT)
[AMBER] Equilibration in multiple steps with decrement in force constants
Carlos Simmerling
(Mon Apr 01 2019 - 11:38:16 PDT)
Priyabrata Das
(Mon Apr 01 2019 - 10:04:08 PDT)
Carlos Simmerling
(Mon Apr 01 2019 - 06:29:41 PDT)
Priyabrata Das
(Mon Apr 01 2019 - 04:30:14 PDT)
Carlos Simmerling
(Mon Apr 01 2019 - 04:11:30 PDT)
Priyabrata Das
(Mon Apr 01 2019 - 03:19:34 PDT)
[AMBER] Error working with pytleap
David A Case
(Mon Apr 08 2019 - 04:44:42 PDT)
ARITRA MITRA
(Mon Apr 08 2019 - 03:58:33 PDT)
[AMBER] Fixing few box dimensions in semiisotropic/anisotropic pressure scaling
David A Case
(Tue Apr 16 2019 - 06:12:08 PDT)
Kyeong-jun Jeong
(Mon Apr 15 2019 - 13:56:54 PDT)
[AMBER] Force field for C-C Di-Tyrosine Linkage
Bharat Manna
(Thu Apr 18 2019 - 03:45:55 PDT)
[AMBER] Force field parameters for modified amino acid residues (carboxy glutamates)
Tanusree S
(Tue Apr 09 2019 - 21:42:30 PDT)
[AMBER] Fwd: AMBER Digest, Vol 2600, Issue 1
SATYAJIT KHATUA
(Mon Apr 01 2019 - 00:45:18 PDT)
[AMBER] Guidance on WHAM
Zachary Fallon
(Thu Apr 18 2019 - 12:35:43 PDT)
Daniel Fernández Remacha
(Thu Apr 18 2019 - 11:28:40 PDT)
Zachary Fallon
(Wed Apr 17 2019 - 10:21:56 PDT)
Daniel Fernández Remacha
(Wed Apr 17 2019 - 03:59:17 PDT)
Carlos Simmerling
(Tue Apr 16 2019 - 12:43:34 PDT)
Zachary Fallon
(Tue Apr 16 2019 - 12:23:01 PDT)
Daniel Fernández Remacha
(Sat Apr 13 2019 - 06:19:01 PDT)
[AMBER] How the instantaneous temperature is calculated in Amber ?
Marek Maly
(Mon Apr 01 2019 - 10:37:31 PDT)
Carlos Simmerling
(Mon Apr 01 2019 - 04:16:16 PDT)
Marek Maly
(Sun Mar 31 2019 - 20:20:18 PDT)
Marek Maly
(Sun Mar 31 2019 - 20:02:36 PDT)
Marek Maly
(Sun Mar 31 2019 - 17:35:05 PDT)
[AMBER] How to build the central fragment of a modified nucleotide in the AMBER force fields
21818674.zju.edu.cn
(Sun Mar 31 2019 - 19:28:55 PDT)
[AMBER] How to select dihedral angles to reweight accelerated molecular dynamics simulation of protein
Mayank Dixit
(Thu Apr 18 2019 - 07:47:04 PDT)
Chetna Tyagi
(Wed Apr 17 2019 - 00:57:18 PDT)
Mayank Dixit
(Tue Apr 16 2019 - 17:48:47 PDT)
[AMBER] How to source oldff in tleap
David A Case
(Fri Apr 12 2019 - 05:47:29 PDT)
Carlos Simmerling
(Fri Apr 12 2019 - 05:00:25 PDT)
Saikat Pal
(Fri Apr 12 2019 - 04:43:24 PDT)
Saikat Pal
(Fri Apr 12 2019 - 04:32:54 PDT)
[AMBER] How to use GaMD in amber16
ATUL KUMAR
(Tue Apr 16 2019 - 01:35:25 PDT)
[AMBER] huge reference.frc in MMPBSA
Antoine Marion
(Sun Mar 31 2019 - 21:20:27 PDT)
[AMBER] Issue with cpptraj.MPI
Daniel Roe
(Tue Apr 23 2019 - 06:34:31 PDT)
Benard, Dany
(Tue Apr 23 2019 - 06:01:36 PDT)
Pratul Agarwal
(Tue Apr 23 2019 - 05:58:41 PDT)
Daniel Roe
(Tue Apr 23 2019 - 05:52:46 PDT)
Pratul Agarwal
(Tue Apr 23 2019 - 05:52:05 PDT)
Benard, Dany
(Tue Apr 23 2019 - 05:44:23 PDT)
[AMBER] issues with pmemd.cuda
Veenis, Andrew Jay
(Fri Apr 26 2019 - 07:08:02 PDT)
David A Case
(Thu Apr 25 2019 - 10:43:32 PDT)
Veenis, Andrew Jay
(Thu Apr 25 2019 - 08:11:46 PDT)
[AMBER] KeyError: 4018 for iron containing enzyme (prolyl hydroxylase)
Mahesh kumar Teli
(Wed Apr 03 2019 - 19:14:48 PDT)
Aashish Bhatt
(Wed Apr 03 2019 - 05:48:11 PDT)
Mahesh kumar Teli
(Tue Apr 02 2019 - 22:06:32 PDT)
[AMBER] leap duplicates bond ('triangular' bond) warning
Pietro Aronica
(Tue Apr 02 2019 - 05:45:04 PDT)
Fabian Glaser
(Tue Apr 02 2019 - 05:16:39 PDT)
[AMBER] Ligand Splitting Issue
David Case
(Sun Apr 07 2019 - 18:22:03 PDT)
Tamsila Parveen
(Sun Apr 07 2019 - 04:21:59 PDT)
[AMBER] location related redox-potential?
Feng, Zimin
(Sun Apr 07 2019 - 14:34:05 PDT)
Cruzeiro,Vinicius Wilian D
(Fri Apr 05 2019 - 16:31:36 PDT)
Feng, Zimin
(Fri Apr 05 2019 - 09:15:00 PDT)
[AMBER] mdgx CreateBellyMask error
David Cerutti
(Mon Apr 15 2019 - 08:02:08 PDT)
Anthony Bogetti
(Mon Apr 15 2019 - 07:50:02 PDT)
[AMBER] metal parameters
Pengfei Li
(Sat Apr 06 2019 - 14:39:29 PDT)
Fabian Glaser
(Fri Apr 05 2019 - 21:56:51 PDT)
[AMBER] metal-oxide-metal interactions
Pengfei Li
(Thu Apr 04 2019 - 17:44:44 PDT)
[AMBER] Mg2+_preparation_general_rule
Antonio Amber Carlesso
(Wed Apr 17 2019 - 09:53:47 PDT)
Antonio Amber Carlesso
(Wed Apr 17 2019 - 08:27:11 PDT)
[AMBER] MM PBSA - clarification
Thomas Evangelidis
(Mon Apr 22 2019 - 06:31:00 PDT)
Prasanth G, Research Scholar
(Sun Apr 21 2019 - 23:17:41 PDT)
Ray Luo
(Fri Apr 19 2019 - 06:35:12 PDT)
Prasanth G, Research Scholar
(Fri Apr 19 2019 - 06:14:33 PDT)
[AMBER] mmpbsa
Chris Moth
(Tue Apr 09 2019 - 19:30:18 PDT)
MYRIAN TORRES RICO
(Tue Apr 09 2019 - 01:22:16 PDT)
[AMBER] mmpbsa error
MYRIAN TORRES RICO
(Tue Apr 30 2019 - 09:28:57 PDT)
David A Case
(Tue Apr 30 2019 - 04:28:17 PDT)
MYRIAN TORRES RICO
(Tue Apr 30 2019 - 02:01:54 PDT)
Daniel Roe
(Fri Apr 05 2019 - 08:06:08 PDT)
MYRIAN TORRES RICO
(Thu Apr 04 2019 - 02:07:07 PDT)
MYRIAN TORRES RICO
(Thu Apr 04 2019 - 01:08:44 PDT)
[AMBER] mol2 files for FEW
Zhonghua Xia
(Tue Apr 30 2019 - 07:48:28 PDT)
David A Case
(Wed Apr 17 2019 - 05:06:50 PDT)
Zhonghua Xia
(Wed Apr 17 2019 - 01:33:24 PDT)
[AMBER] More macOS compilation issues....
Gustaf Olsson
(Fri Apr 26 2019 - 22:48:25 PDT)
David A Case
(Fri Apr 26 2019 - 06:48:32 PDT)
Gustaf Olsson
(Thu Apr 25 2019 - 23:49:37 PDT)
Gustaf Olsson
(Thu Apr 25 2019 - 13:08:51 PDT)
Gustaf Olsson
(Mon Apr 22 2019 - 22:20:11 PDT)
David A Case
(Mon Apr 22 2019 - 13:07:11 PDT)
Gustaf Olsson
(Sun Apr 21 2019 - 13:37:05 PDT)
Gustaf Olsson
(Sun Apr 21 2019 - 03:31:39 PDT)
David A Case
(Thu Apr 18 2019 - 10:33:25 PDT)
Hai Nguyen
(Thu Apr 18 2019 - 06:47:08 PDT)
Gustaf Olsson
(Thu Apr 18 2019 - 01:20:39 PDT)
[AMBER] namd and amber md energies do not match
Akshay Prabhakant
(Mon Apr 15 2019 - 23:00:28 PDT)
David A Case
(Fri Apr 12 2019 - 05:37:56 PDT)
Akshay Prabhakant
(Thu Apr 11 2019 - 11:33:01 PDT)
[AMBER] Negative dihedral angle n glycan simulation
Rajarshi Roy
(Fri Apr 26 2019 - 19:20:08 PDT)
Lachele Foley
(Fri Apr 26 2019 - 18:10:18 PDT)
Rajarshi Roy
(Thu Apr 11 2019 - 10:01:20 PDT)
Rajarshi Roy
(Thu Apr 11 2019 - 09:45:11 PDT)
Irfan Alibay
(Thu Apr 11 2019 - 04:43:51 PDT)
Lachele Foley
(Wed Apr 10 2019 - 12:13:57 PDT)
Lachele Foley
(Tue Apr 09 2019 - 10:32:58 PDT)
Rajarshi Roy
(Tue Apr 09 2019 - 00:55:44 PDT)
Lachele Foley
(Mon Apr 08 2019 - 08:49:58 PDT)
Lachele Foley
(Mon Apr 08 2019 - 08:24:16 PDT)
Rajarshi Roy
(Tue Apr 02 2019 - 04:04:58 PDT)
[AMBER] New compile-issue macOS, CPPTRAJ
Gustaf Olsson
(Mon Apr 08 2019 - 06:48:20 PDT)
David A Case
(Mon Apr 08 2019 - 04:57:11 PDT)
David A Case
(Fri Apr 05 2019 - 06:01:56 PDT)
Gustaf Olsson
(Thu Apr 04 2019 - 06:54:53 PDT)
Daniel Roe
(Thu Apr 04 2019 - 06:30:51 PDT)
Gustaf Olsson
(Thu Apr 04 2019 - 06:16:01 PDT)
David A Case
(Wed Apr 03 2019 - 07:36:59 PDT)
Hai Nguyen
(Wed Apr 03 2019 - 05:59:45 PDT)
Hai Nguyen
(Wed Apr 03 2019 - 05:54:30 PDT)
David A Case
(Wed Apr 03 2019 - 05:24:27 PDT)
Gustaf Olsson
(Tue Apr 02 2019 - 23:36:19 PDT)
Hai Nguyen
(Tue Apr 02 2019 - 07:20:23 PDT)
Gustaf Olsson
(Tue Apr 02 2019 - 06:40:03 PDT)
Hai Nguyen
(Tue Apr 02 2019 - 06:26:56 PDT)
Gustaf Olsson
(Tue Apr 02 2019 - 06:23:48 PDT)
Gustaf Olsson
(Tue Apr 02 2019 - 00:27:58 PDT)
Daniel Roe
(Mon Apr 01 2019 - 08:18:46 PDT)
David A Case
(Mon Apr 01 2019 - 07:45:28 PDT)
Gustaf Olsson
(Mon Apr 01 2019 - 05:04:14 PDT)
[AMBER] NFE error: Cannot read &abmd namelist
Feng Pan
(Tue Apr 02 2019 - 16:56:47 PDT)
Jason Imamoto
(Mon Apr 01 2019 - 00:54:59 PDT)
[AMBER] Novel Force Field Parameters for Aromatic Dihedrals
Erdem Yeler
(Sun Apr 28 2019 - 13:09:41 PDT)
[AMBER] NpT simulations in interfacial system
David Case
(Sun Apr 28 2019 - 09:56:50 PDT)
Lucas Bandeira
(Sat Apr 27 2019 - 07:38:33 PDT)
[AMBER] outtraj question
Daniel Roe
(Tue Apr 30 2019 - 07:23:30 PDT)
Xiaoyu Wang
(Fri Apr 05 2019 - 15:35:10 PDT)
[AMBER] parameters for isolated zwitter ion tyrosine
Elvis Martis
(Wed Apr 10 2019 - 23:50:29 PDT)
angad sharma
(Wed Apr 10 2019 - 23:15:25 PDT)
[AMBER] Patches for AmberTools18
Hai Nguyen
(Wed Apr 10 2019 - 13:19:11 PDT)
Stephan Schott
(Wed Apr 10 2019 - 05:38:58 PDT)
viktor drobot
(Wed Apr 10 2019 - 04:26:12 PDT)
[AMBER] pdb4amber install w/ conda
Hai Nguyen
(Fri Apr 12 2019 - 23:14:10 PDT)
Hai Nguyen
(Fri Apr 12 2019 - 09:49:23 PDT)
Paul, Austin
(Fri Apr 12 2019 - 09:16:21 PDT)
[AMBER] pKa calculation
Tanmoy Paul
(Tue Apr 16 2019 - 23:18:58 PDT)
[AMBER] pmemd.CUDA vs pmemd.MPI for equilibration of protein-ligand and trajectory identification for mmpbsa
Prasanth G, Research Scholar
(Fri Apr 05 2019 - 23:47:01 PDT)
[AMBER] possible bug in charmmlipid2amber.py
liu junjun
(Mon Apr 22 2019 - 00:14:17 PDT)
[AMBER] preparing a new pdb
Boutheïna KERKENI
(Sun Apr 07 2019 - 03:56:11 PDT)
[AMBER] Problem calculating water density over distance
Lucas Bandeira
(Thu Apr 04 2019 - 13:35:38 PDT)
[AMBER] Problem calculating water mass density over distance
Gerardo Zerbetto De Palma
(Thu Apr 11 2019 - 07:54:08 PDT)
Lucas Bandeira
(Thu Apr 11 2019 - 09:48:23 PDT)
Gerardo Zerbetto De Palma
(Thu Apr 11 2019 - 09:37:30 PDT)
Lucas Bandeira
(Thu Apr 11 2019 - 09:08:47 PDT)
Gerardo Zerbetto De Palma
(Thu Apr 11 2019 - 09:05:18 PDT)
Lucas Bandeira
(Thu Apr 11 2019 - 09:00:23 PDT)
[AMBER] problem in locating Aqvist Mg2+ parameter in amber
David Case
(Tue Apr 23 2019 - 05:23:49 PDT)
ATUL KUMAR
(Mon Apr 22 2019 - 21:52:18 PDT)
[AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine
Xiaoting Mao
(Sat Apr 13 2019 - 02:48:14 PDT)
[AMBER] Problem in setting parameters for the modified nucleotide
Xiaoting Mao
(Mon Apr 08 2019 - 06:10:58 PDT)
[AMBER] Problem with heating the system
Pratul Agarwal
(Wed Apr 24 2019 - 05:14:12 PDT)
ATUL KUMAR
(Wed Apr 24 2019 - 04:53:58 PDT)
David A Case
(Wed Apr 24 2019 - 04:47:18 PDT)
ATUL KUMAR
(Wed Apr 24 2019 - 02:06:52 PDT)
Bill Ross
(Wed Apr 24 2019 - 01:49:56 PDT)
ATUL KUMAR
(Wed Apr 24 2019 - 01:57:34 PDT)
[AMBER] Problems calculating density over distance
Lucas Bandeira
(Mon Apr 01 2019 - 09:13:25 PDT)
[AMBER] Problems in forcefield parameterization of Mercury
Pengfei Li
(Fri Apr 19 2019 - 08:42:20 PDT)
Muthukumaran Rajagopalan
(Tue Apr 16 2019 - 22:36:14 PDT)
Pengfei Li
(Tue Apr 16 2019 - 18:31:35 PDT)
Muthukumaran Rajagopalan
(Tue Apr 16 2019 - 10:24:35 PDT)
[AMBER] Problems in setting parameters for the modified nucleotide
Xiaoting Mao
(Fri Apr 12 2019 - 06:08:43 PDT)
[AMBER] processing trajectories subjected to GIST analysis
Daniel Roe
(Tue Apr 30 2019 - 06:58:42 PDT)
Alfredo Quevedo
(Tue Apr 23 2019 - 23:19:47 PDT)
[AMBER] Question about chemical reaction in vacuum with adding an extra reaction field (Specify dielectric constant in vacuum)
王婷婷
(Thu Apr 11 2019 - 18:40:46 PDT)
David A Case
(Thu Apr 11 2019 - 06:57:52 PDT)
王婷婷
(Wed Apr 10 2019 - 18:03:59 PDT)
[AMBER] Question about NEB
Lillian Chong
(Fri Apr 12 2019 - 06:02:57 PDT)
[AMBER] Question about QM/MM simulation in vacuum connecting Amber and Gaussian 09 package
Roitberg,Adrian E
(Mon Apr 08 2019 - 17:41:56 PDT)
王婷婷
(Mon Apr 08 2019 - 17:36:31 PDT)
[AMBER] Regarding cosine content calculation in AMBER
Rajarshi Roy
(Tue Apr 30 2019 - 10:39:37 PDT)
Pratul Agarwal
(Tue Apr 30 2019 - 09:46:56 PDT)
Rajarshi Roy
(Tue Apr 30 2019 - 09:14:09 PDT)
Pratul Agarwal
(Tue Apr 30 2019 - 08:53:56 PDT)
Rajarshi Roy
(Tue Apr 30 2019 - 08:47:39 PDT)
Daniel Roe
(Tue Apr 30 2019 - 06:16:45 PDT)
Rajarshi Roy
(Mon Apr 29 2019 - 22:22:40 PDT)
[AMBER] REGARDING MPI
Charu Sharma (JRF)
(Wed Apr 10 2019 - 11:06:10 PDT)
[AMBER] regarding radius of gyration
Carlos Simmerling
(Mon Apr 22 2019 - 07:02:36 PDT)
angad sharma
(Mon Apr 22 2019 - 06:03:04 PDT)
[AMBER] regarding simulation
David A Case
(Tue Apr 02 2019 - 05:20:38 PDT)
Charu Sharma (JRF)
(Tue Apr 02 2019 - 00:55:53 PDT)
[AMBER] Release of AmberTools19
David Case
(Fri Apr 26 2019 - 17:59:43 PDT)
[AMBER] rms2d analysis
Debarati DasGupta
(Wed Apr 03 2019 - 06:20:20 PDT)
Daniel Roe
(Tue Apr 02 2019 - 12:43:54 PDT)
Debarati DasGupta
(Tue Apr 02 2019 - 11:38:26 PDT)
[AMBER] RTX 2070 GPU Card
Ajeet Kumar Yadav
(Mon Apr 15 2019 - 03:02:01 PDT)
[AMBER] RTX-2070 supported(untested)?
Bill Ross
(Fri Apr 19 2019 - 05:11:25 PDT)
Carlos Simmerling
(Fri Apr 19 2019 - 05:05:48 PDT)
David Cerutti
(Thu Apr 18 2019 - 14:28:33 PDT)
Yeyue Xiong
(Thu Apr 18 2019 - 13:29:28 PDT)
[AMBER] Save RST from mdcrd containing velocities
Daniel Roe
(Thu Apr 18 2019 - 10:59:21 PDT)
Yuliana Bosken
(Sat Apr 13 2019 - 02:40:05 PDT)
[AMBER] saving output of Gaussian accelerated MD
Qinghua Liao
(Tue Apr 23 2019 - 07:41:28 PDT)
[AMBER] secondary structure
Carlos Simmerling
(Wed Apr 24 2019 - 04:59:50 PDT)
angad sharma
(Wed Apr 24 2019 - 04:32:53 PDT)
[AMBER] secstruct issue in CPPTRAJ
Daniel Roe
(Tue Apr 16 2019 - 05:26:58 PDT)
Daniel Roe
(Wed Apr 10 2019 - 12:16:06 PDT)
Daniel Roe
(Wed Apr 10 2019 - 11:28:42 PDT)
SARAH JEANNE LEFAVE
(Mon Apr 08 2019 - 13:22:18 PDT)
[AMBER] setting up triplicate runs
David Cerutti
(Thu Apr 25 2019 - 19:02:45 PDT)
Yin, Guowei
(Thu Apr 25 2019 - 18:08:00 PDT)
[AMBER] silver parameters
Christina Bergonzo
(Fri Apr 12 2019 - 06:48:50 PDT)
Uroš Javornik
(Fri Apr 12 2019 - 06:29:12 PDT)
[AMBER] Simulation with Protein, cofactor and Ligand
Prasanth G, Research Scholar
(Thu Apr 25 2019 - 11:41:05 PDT)
[AMBER] smflags in configure script
David A Case
(Mon Apr 22 2019 - 13:03:56 PDT)
Charles Lin
(Mon Apr 22 2019 - 12:52:10 PDT)
viktor drobot
(Fri Apr 19 2019 - 07:19:24 PDT)
[AMBER] styrene sulfonate molecule building using xleap
David A Case
(Wed Apr 24 2019 - 04:45:08 PDT)
Shilpa Gupta
(Tue Apr 23 2019 - 23:32:36 PDT)
[AMBER] Suggestions on running a qm-mm simulation for studying a group transfer reaction
Prayagraj Fandilolu
(Mon Apr 22 2019 - 05:43:24 PDT)
[AMBER] T4 vs RTX2080Ti
David Cerutti
(Fri Apr 12 2019 - 08:21:38 PDT)
Shenglong Wang
(Thu Apr 11 2019 - 08:03:00 PDT)
Giovanni Grazioso
(Thu Apr 11 2019 - 08:00:42 PDT)
[AMBER] Targeted MD
Carlos Simmerling
(Thu Apr 25 2019 - 05:01:37 PDT)
Elena Gomez
(Thu Apr 25 2019 - 01:08:18 PDT)
[AMBER] tests with different # of threads
Vaibhav Dixit
(Thu Apr 04 2019 - 08:11:38 PDT)
David A Case
(Wed Apr 03 2019 - 05:30:44 PDT)
Vaibhav Dixit
(Wed Apr 03 2019 - 03:26:04 PDT)
[AMBER] trouble in amberFATA: Atom doesn't have a type
Sally Pias
(Fri Apr 19 2019 - 12:09:19 PDT)
Maximilien BERNE
(Fri Apr 19 2019 - 09:19:14 PDT)
[AMBER] varying pressure conditions?
Carlos Simmerling
(Mon Apr 01 2019 - 08:23:06 PDT)
Shayna Hilburg
(Mon Apr 01 2019 - 08:21:07 PDT)
[AMBER] WHAM umbrella PMF of ligand Z diffusion on lipid molecule
zmatovic.kg.ac.rs
(Mon Apr 29 2019 - 04:05:27 PDT)
[AMBER] Why is SPAM throwing errors when I see none in my input files or trajectories.
Daniel Roe
(Tue Apr 30 2019 - 06:12:07 PDT)
Debarati DasGupta
(Mon Apr 29 2019 - 13:25:58 PDT)
[AMBER] xleap display
Gustaf Olsson
(Sun Apr 28 2019 - 05:58:47 PDT)
Bill Ross
(Sat Apr 27 2019 - 21:28:56 PDT)
Yin, Guowei
(Sat Apr 27 2019 - 19:54:15 PDT)
Bill Ross
(Sat Apr 27 2019 - 16:31:50 PDT)
Pratul Agarwal
(Sat Apr 27 2019 - 16:02:31 PDT)
Bill Ross
(Sat Apr 27 2019 - 15:57:41 PDT)
Bill Ross
(Sat Apr 27 2019 - 15:49:56 PDT)
Yin, Guowei
(Sat Apr 27 2019 - 14:49:20 PDT)
secstruct issue in CPPTRAJ
SARAH JEANNE LEFAVE
(Tue Apr 16 2019 - 05:44:35 PDT)
Last message date
:
Tue Apr 30 2019 - 13:00:03 PDT
Archived on
: Sun Dec 01 2024 - 05:55:45 PST
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