Amber Archive Mar 2020 by author
326 messages
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Starting
Sun Mar 01 2020 - 06:00:04 PST,
Ending
Tue Mar 31 2020 - 16:00:02 PDT
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Abhilash J
Re: [AMBER] CUDA single gpu usage issue
(Fri Mar 06 2020 - 13:48:38 PST)
Re: [AMBER] CUDA single gpu usage issue
(Wed Mar 04 2020 - 09:32:00 PST)
Re: [AMBER] CUDA single gpu usage issue
(Tue Mar 03 2020 - 13:58:03 PST)
[AMBER] AMBER 18 compilation error with CUDA 10.2
(Sun Mar 01 2020 - 17:08:23 PST)
Adrian Roitberg
Re: [AMBER] unusual planarity change during md.
(Thu Mar 12 2020 - 08:38:14 PDT)
Re: [AMBER] linear interaction energy tool in AMBER
(Fri Mar 06 2020 - 08:47:52 PST)
Ahmed Elrashedy
Re: [AMBER] checkstructure with cpptraj
(Tue Mar 31 2020 - 11:29:41 PDT)
Re: [AMBER] information regarding space filling visualization
(Sat Mar 14 2020 - 06:04:43 PDT)
Akshay Prabhakant
Re: [AMBER] parameters for Si3N4
(Mon Mar 16 2020 - 21:11:06 PDT)
[AMBER] linear interaction energy tool in AMBER
(Thu Mar 05 2020 - 21:24:01 PST)
Alessandro Contini
Re: [AMBER] replica exchange with GPU
(Mon Mar 02 2020 - 02:43:16 PST)
Ana Ziad
Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem
(Sat Mar 21 2020 - 08:50:07 PDT)
Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem
(Fri Mar 20 2020 - 10:29:33 PDT)
Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem
(Fri Mar 20 2020 - 09:20:00 PDT)
[AMBER] issue while installing AMBER tools on windows10 Linux subsystem
(Tue Mar 17 2020 - 14:35:54 PDT)
Andrea H. Kasun
Re: [AMBER] Problems with Nvidia Drivers
(Sun Mar 29 2020 - 04:14:24 PDT)
Re: [AMBER] Problems with Nvidia Drivers
(Sat Mar 28 2020 - 03:21:02 PDT)
[AMBER] Problems with Nvidia Drivers
(Thu Mar 26 2020 - 10:25:16 PDT)
ankita mehta
Re: [AMBER] PDB Modification
(Mon Mar 30 2020 - 08:55:23 PDT)
[AMBER] PDB Modification
(Mon Mar 30 2020 - 06:43:50 PDT)
Re: [AMBER] Error while amber installation
(Sat Mar 28 2020 - 23:26:38 PDT)
[AMBER] Error while amber installation
(Sat Mar 28 2020 - 10:12:56 PDT)
Re: [AMBER] Modified force fields
(Tue Mar 10 2020 - 10:26:47 PDT)
[AMBER] Modified force fields
(Mon Mar 09 2020 - 09:40:12 PDT)
Re: [AMBER] Modified force fields
(Sun Mar 08 2020 - 20:52:39 PDT)
Re: [AMBER] Modified force fields
(Sun Mar 08 2020 - 10:59:09 PDT)
[AMBER] Modified force fields
(Thu Mar 05 2020 - 20:34:37 PST)
Antonio Amber Carlesso
[AMBER] MM-PB(GB)/SA error message
(Tue Mar 24 2020 - 07:41:12 PDT)
[AMBER] cross angle analysis
(Tue Mar 24 2020 - 05:56:28 PDT)
Azahara.Doncel.uv.es
[AMBER] mmpbsa_py_energy failed with prmtop dim_gas.prmtop
(Fri Mar 27 2020 - 09:11:29 PDT)
[AMBER] mmpbsa_py_energy failed with prmtop dim_gas.prmtop
(Thu Mar 12 2020 - 08:58:17 PDT)
bbalta.itu.edu.tr
Re: [AMBER] replica exchange with GPU
(Mon Mar 02 2020 - 01:21:20 PST)
Busra Demir
Re: [AMBER] QM/MM Convergence questions
(Thu Mar 05 2020 - 03:41:27 PST)
Carlos Simmerling
Re: [AMBER] Amber restart simulation
(Tue Mar 31 2020 - 04:57:19 PDT)
Re: [AMBER] Abasic Site and Leap Polymerization
(Mon Mar 30 2020 - 10:14:03 PDT)
Re: [AMBER] NPT equilibration is crashing
(Sun Mar 29 2020 - 03:19:23 PDT)
Re: [AMBER] setting pdb file
(Fri Mar 20 2020 - 16:55:37 PDT)
Re: [AMBER] setting pdb file
(Fri Mar 20 2020 - 12:55:57 PDT)
Re: [AMBER] If a non-standard force field is used for proteins, how would you approach parameterization of lipids and ligands?
(Tue Mar 17 2020 - 03:18:53 PDT)
Re: [AMBER] About the D form amino amber force field
(Sun Mar 15 2020 - 03:42:44 PDT)
Re: [AMBER] GAFF/AMBER peptide bond
(Sat Mar 14 2020 - 15:06:51 PDT)
Re: [AMBER] Lone Pairs in AMBER FF
(Sat Mar 14 2020 - 08:18:40 PDT)
Re: [AMBER] information regarding space filling visualization
(Sat Mar 14 2020 - 02:50:36 PDT)
Re: [AMBER] simulations of proteins with 2 domains connected by a linker
(Thu Mar 12 2020 - 06:58:25 PDT)
Re: [AMBER] What's the least biased way to stop a molecule from crossing a periodic boundary?
(Thu Mar 12 2020 - 04:48:44 PDT)
Re: [AMBER] What's the least biased way to stop a molecule from crossing a periodic boundary?
(Thu Mar 12 2020 - 04:21:40 PDT)
Re: [AMBER] Modified AA residue without NH2 end.
(Thu Mar 12 2020 - 03:51:55 PDT)
Re: [AMBER] REMD hybrid solvent model
(Wed Mar 11 2020 - 10:32:33 PDT)
Re: [AMBER] REMD hybrid solvent model
(Wed Mar 11 2020 - 08:39:32 PDT)
Re: [AMBER] What is the default pH when loading a protein in Amber environment
(Wed Mar 11 2020 - 04:48:30 PDT)
Re: [AMBER] REMD hybrid solvent model
(Tue Mar 10 2020 - 19:09:09 PDT)
Re: [AMBER] Modified force fields
(Tue Mar 10 2020 - 10:53:10 PDT)
Re: [AMBER] Modified force fields
(Mon Mar 09 2020 - 09:45:00 PDT)
Re: [AMBER] Issue in drug parameter
(Sun Mar 01 2020 - 14:34:48 PST)
Chetna Tyagi
[AMBER] units of the calculated diffusion coefficient
(Wed Mar 11 2020 - 10:54:27 PDT)
Christina Bergonzo
Re: [AMBER] Abasic Site and Leap Polymerization
(Mon Mar 30 2020 - 11:21:43 PDT)
Re: [AMBER] Abasic Site and Leap Polymerization
(Mon Mar 30 2020 - 08:07:58 PDT)
Re: [AMBER] ff19SB + BSC1 + OPC + which ions ?
(Sun Mar 29 2020 - 14:28:35 PDT)
Re: [AMBER] Citing DNA OL15 forcefield
(Wed Mar 04 2020 - 11:55:02 PST)
Re: [AMBER] tar-MD with custom J-coupling relation
(Tue Mar 03 2020 - 06:02:34 PST)
Clorice Reinhardt
Re: [AMBER] sum of charges from parm file
(Tue Mar 31 2020 - 15:40:38 PDT)
Cruzeiro,Vinicius Wilian D
Re: [AMBER] replica exchange with GPU
(Mon Mar 02 2020 - 08:45:44 PST)
Daniel Roe
Re: [AMBER] MPI+threads in Amber
(Tue Mar 31 2020 - 10:35:49 PDT)
Re: [AMBER] checkstructure with cpptraj
(Tue Mar 31 2020 - 10:31:51 PDT)
Re: [AMBER] nastruct and modified base pairs
(Fri Mar 27 2020 - 06:00:00 PDT)
Re: [AMBER] nastruct and modified base pairs
(Thu Mar 26 2020 - 12:30:55 PDT)
Re: [AMBER] nastruct and modified base pairs
(Wed Mar 25 2020 - 12:42:00 PDT)
Re: [AMBER] cross angle analysis
(Wed Mar 25 2020 - 12:39:23 PDT)
Re: [AMBER] Ambmask Error in group input::atommask.f::pop_evalstack stack underflow
(Wed Mar 25 2020 - 12:30:44 PDT)
Re: [AMBER] Clustering analysis
(Wed Mar 25 2020 - 12:27:27 PDT)
Re: [AMBER] DBscan gives me errors in clustering
(Wed Mar 25 2020 - 12:18:53 PDT)
Re: [AMBER] sieve keyword in cpptraj clustering
(Wed Mar 25 2020 - 12:16:43 PDT)
Re: [AMBER] setting pdb file
(Fri Mar 20 2020 - 12:29:27 PDT)
Re: [AMBER] EXTRACTING A PARTICULAR FRAME
(Thu Mar 12 2020 - 10:53:29 PDT)
Re: [AMBER] units of the calculated diffusion coefficient
(Thu Mar 12 2020 - 10:48:55 PDT)
Re: [AMBER] EXTRACTING A PARTICULAR FRAME
(Thu Mar 12 2020 - 10:45:38 PDT)
Re: [AMBER] Inconsistency in energy values between out files and cpptraj
(Tue Mar 10 2020 - 09:07:51 PDT)
Re: [AMBER] Incosistency in energy values from out files and cpptraj energy tools
(Tue Mar 10 2020 - 08:54:41 PDT)
David A Case
Re: [AMBER] Error: Could not find angle parameter
(Sun Mar 29 2020 - 07:41:39 PDT)
Re: [AMBER] ff19SB + BSC1 + OPC + which ions ?
(Sun Mar 29 2020 - 07:36:29 PDT)
Re: [AMBER] Error while amber installation
(Sat Mar 28 2020 - 16:47:06 PDT)
Re: [AMBER] AmberTools19 update.8 fails to install
(Sat Mar 28 2020 - 08:21:49 PDT)
Re: [AMBER] residue library for na_link AmberTools19
(Thu Mar 26 2020 - 05:10:41 PDT)
Re: [AMBER] tleap for Mg2+ data type
(Wed Mar 25 2020 - 19:09:01 PDT)
Re: [AMBER] FATAL Error: Atom does not have a type (Cation)
(Wed Mar 25 2020 - 19:01:11 PDT)
Re: [AMBER] FATAL Error: Atom does not have a type (Cation)
(Wed Mar 25 2020 - 18:51:25 PDT)
Re: [AMBER] parameterization with crystal water
(Wed Mar 25 2020 - 18:41:55 PDT)
Re: [AMBER] Installation problem for a parallel version of Amber18/AmberTools19
(Mon Mar 23 2020 - 06:38:48 PDT)
Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem
(Fri Mar 20 2020 - 10:09:23 PDT)
Re: [AMBER] about TREE_CHAIN_CLASSIFICATION
(Fri Mar 20 2020 - 06:11:51 PDT)
Re: [AMBER] A problem of "Could not import Amber Python modules"
(Wed Mar 18 2020 - 05:51:21 PDT)
Re: [AMBER] Boron compunds with "pdb" file with novel frcmod file
(Sun Mar 15 2020 - 09:41:26 PDT)
Re: [AMBER] Lone Pairs in AMBER FF
(Sun Mar 15 2020 - 06:03:55 PDT)
Re: [AMBER] Questions on force field
(Fri Mar 13 2020 - 04:28:59 PDT)
Re: [AMBER] TI runs on GPU
(Fri Mar 13 2020 - 04:24:39 PDT)
Re: [AMBER] Reg: MMGBSA for NAMD trajectory
(Wed Mar 11 2020 - 11:20:43 PDT)
Re: [AMBER] Found an invalid periodicity in the prmtop file: ... CalcError: bin/mmpbsa_py_energy failed with prmtop .prmtop!
(Tue Mar 10 2020 - 11:44:31 PDT)
Re: [AMBER] Modified force fields
(Tue Mar 10 2020 - 11:38:36 PDT)
Re: [AMBER] AmberTools on Ubuntu 19.04: compilation
(Tue Mar 10 2020 - 05:25:52 PDT)
Re: [AMBER] AmberTools19 install error
(Sun Mar 08 2020 - 09:39:48 PDT)
Re: [AMBER] Modified force fields
(Fri Mar 06 2020 - 05:00:25 PST)
Re: [AMBER] QM/MM Convergence questions
(Fri Mar 06 2020 - 04:51:58 PST)
Re: [AMBER] TI production error in nstep =1
(Fri Mar 06 2020 - 04:48:17 PST)
Re: [AMBER] CUDA single gpu usage issue
(Tue Mar 03 2020 - 07:09:18 PST)
Re: [AMBER] Question of units
(Mon Mar 02 2020 - 18:36:25 PST)
Re: [AMBER] Issue in drug parameter
(Sun Mar 01 2020 - 14:28:39 PST)
Re: [AMBER] Issue in drug parameter
(Sun Mar 01 2020 - 05:32:04 PST)
David Cerutti
Re: [AMBER] Simulations Without Network
(Fri Mar 27 2020 - 09:56:55 PDT)
Re: [AMBER] questions about paramfit and frcmod file
(Sun Mar 22 2020 - 23:36:44 PDT)
Re: [AMBER] RTX 2020 Super GPU Random Memory Errors
(Sat Mar 21 2020 - 15:54:50 PDT)
Re: [AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results?
(Mon Mar 09 2020 - 10:36:58 PDT)
Re: [AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results?
(Fri Mar 06 2020 - 11:10:49 PST)
David Sáez
Re: [AMBER] checkstructure with cpptraj
(Tue Mar 31 2020 - 12:55:49 PDT)
Re: [AMBER] NPT equilibration is crashing
(Sun Mar 29 2020 - 23:52:27 PDT)
Re: [AMBER] NPT equilibration is crashing
(Sat Mar 28 2020 - 22:01:24 PDT)
Re: [AMBER] Are the 6-character atom types of CGenFF compatible with parmed-chamber
(Thu Mar 05 2020 - 15:58:18 PST)
Re: [AMBER] Are the 6-character atom types of CGenFF compatible with parmed-chamber
(Thu Mar 05 2020 - 13:40:46 PST)
[AMBER] Are the 6-character atom types of CGenFF compatible with parmed-chamber
(Wed Mar 04 2020 - 11:33:42 PST)
Debarati DasGupta
[AMBER] Clustering query
(Sun Mar 22 2020 - 10:37:06 PDT)
[AMBER] Clustering analysis
(Wed Mar 18 2020 - 15:33:59 PDT)
Re: [AMBER] TI runs on GPU
(Sun Mar 15 2020 - 06:56:06 PDT)
[AMBER] TI runs on GPU
(Thu Mar 12 2020 - 13:48:29 PDT)
[AMBER] DBscan gives me errors in clustering
(Wed Mar 11 2020 - 08:40:34 PDT)
[AMBER] sieve keyword in cpptraj clustering
(Tue Mar 10 2020 - 06:36:59 PDT)
[AMBER] 2DRMS before clustering
(Sat Mar 07 2020 - 08:46:56 PST)
Re: [AMBER] TI production error in nstep =1
(Fri Mar 06 2020 - 06:46:40 PST)
[AMBER] TI production error in nstep =1
(Thu Mar 05 2020 - 13:38:21 PST)
[AMBER] dvdl.dat file details AMBER18 TI
(Tue Mar 03 2020 - 07:48:35 PST)
Dieter Buyst
[AMBER] tar-MD with custom J-coupling relation
(Tue Mar 03 2020 - 05:37:30 PST)
Elvis Martis
Re: [AMBER] Clustering query
(Sun Mar 22 2020 - 11:14:19 PDT)
Re: [AMBER] information regarding space filling visualization
(Sat Mar 14 2020 - 02:49:08 PDT)
Re: [AMBER] Question about MMPBSA calculation
(Mon Mar 09 2020 - 03:41:42 PDT)
emanuele falbo
Re: [AMBER] Writing Trajectories as netcdf files
(Wed Mar 25 2020 - 10:16:46 PDT)
Re: [AMBER] AmberTools on Ubuntu 19.04: compilation
(Tue Mar 10 2020 - 08:43:32 PDT)
[AMBER] AmberTools on Ubuntu 19.04: compilation
(Tue Mar 10 2020 - 03:16:28 PDT)
Erdem Yeler
Re: [AMBER] Boron compunds with "pdb" file with novel frcmod file
(Tue Mar 17 2020 - 05:56:31 PDT)
[AMBER] Boron compunds with "pdb" file with novel frcmod file
(Sat Mar 14 2020 - 13:43:33 PDT)
Re: [AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results?
(Thu Mar 12 2020 - 00:33:01 PDT)
Re: [AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results?
(Mon Mar 09 2020 - 05:34:01 PDT)
Re: [AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results?
(Mon Mar 09 2020 - 02:10:48 PDT)
[AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results?
(Fri Mar 06 2020 - 04:11:20 PST)
Feng Pan
Re: [AMBER] ** NFE-Error ** : Cannot read &colvar namelist!
(Mon Mar 23 2020 - 12:18:32 PDT)
Filipa Mendonça
[AMBER] KeyError: 'MG'
(Wed Mar 04 2020 - 09:00:33 PST)
Gabriel Jara
[AMBER] problems implementing tiMerge for base pair mutation
(Thu Mar 12 2020 - 10:18:00 PDT)
Garcia, Mauro
Re: [AMBER] Simulations Without Network
(Fri Mar 27 2020 - 15:31:29 PDT)
[AMBER] Simulations Without Network
(Fri Mar 27 2020 - 09:34:57 PDT)
geyushu.ustc.edu.cn
[AMBER] AMBER19: error in reading namelist cntrl
(Mon Mar 09 2020 - 03:04:38 PDT)
Giorgos Lambrinidis
Re: [AMBER] RTX 2020 Super GPU Random Memory Errors
(Sun Mar 22 2020 - 02:56:10 PDT)
[AMBER] RTX 2020 Super GPU Random Memory Errors
(Sat Mar 21 2020 - 12:43:43 PDT)
[AMBER] RTX 2020 Super GPU Random Memorry Errors
(Sat Mar 21 2020 - 12:36:07 PDT)
Goetz, Andreas
Re: [AMBER] How to setup a QM/MM calculation in Amber
(Fri Mar 27 2020 - 17:23:32 PDT)
Re: [AMBER] QM/MM Convergence questions
(Mon Mar 09 2020 - 12:17:48 PDT)
Gustaf Olsson
Re: [AMBER] checkstructure with cpptraj
(Sun Mar 29 2020 - 12:47:08 PDT)
Re: [AMBER] Simulations Without Network
(Fri Mar 27 2020 - 13:21:09 PDT)
Re: [AMBER] SImulation prepared using CHARMM GUI terminates with no error at the NTP step
(Wed Mar 25 2020 - 23:58:56 PDT)
Re: [AMBER] Installation problem for a parallel version of Amber18/AmberTools19
(Tue Mar 24 2020 - 23:46:19 PDT)
Re: [AMBER] setting pdb file
(Fri Mar 20 2020 - 15:52:25 PDT)
Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem
(Fri Mar 20 2020 - 15:49:39 PDT)
Re: [AMBER] setting pdb file
(Fri Mar 20 2020 - 15:31:17 PDT)
Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem
(Wed Mar 18 2020 - 14:03:04 PDT)
Re: [AMBER] AmberTools19 serial installation test errors
(Fri Mar 13 2020 - 01:52:28 PDT)
Re: [AMBER] EXTRACTING A PARTICULAR FRAME
(Thu Mar 12 2020 - 02:06:09 PDT)
Re: [AMBER] EXTRACTING A PARTICULAR FRAME
(Thu Mar 12 2020 - 01:00:21 PDT)
Re: [AMBER] AMBER19: error in reading namelist cntrl
(Mon Mar 09 2020 - 03:10:58 PDT)
Re: [AMBER] AmberTools19 install error
(Sun Mar 08 2020 - 14:37:42 PDT)
Re: [AMBER] error job.sh
(Thu Mar 05 2020 - 09:35:29 PST)
Gustavo Seabra
Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial
(Fri Mar 27 2020 - 21:31:38 PDT)
[AMBER] "Error of reading the .dat file" in MCPB.py step 2
(Fri Mar 20 2020 - 14:42:18 PDT)
Gül Zerze
Re: [AMBER] residue library for na_link AmberTools19
(Thu Mar 26 2020 - 10:33:34 PDT)
[AMBER] residue library for na_link AmberTools19
(Wed Mar 25 2020 - 18:38:27 PDT)
Hanne Antila
[AMBER] Differences in Lennard-Jones interactions in CPU vs GPU pmemd?
(Mon Mar 30 2020 - 09:26:43 PDT)
Harold Grosjean
[AMBER] Found an invalid periodicity in the prmtop file: ... CalcError: bin/mmpbsa_py_energy failed with prmtop .prmtop!
(Tue Mar 10 2020 - 10:47:02 PDT)
Himanshu Joshi
Re: [AMBER] tleap/xleap performance enhancement
(Wed Mar 04 2020 - 10:13:11 PST)
Hira Jabeen
[AMBER] parameterization with crystal water
(Wed Mar 25 2020 - 10:53:52 PDT)
HOCHEOL LIM
[AMBER] Amber parameters for heme b / d coordinated with deprotonated tyrosine
(Thu Mar 05 2020 - 22:45:31 PST)
Homeo Morphism
[AMBER] If a non-standard force field is used for proteins, how would you approach parameterization of lipids and ligands?
(Tue Mar 17 2020 - 01:24:28 PDT)
[AMBER] What's the least biased way to stop a molecule from crossing a periodic boundary?
(Thu Mar 12 2020 - 04:16:23 PDT)
Hosein Geraili Daronkola
Re: [AMBER] REMD hybrid solvent model
(Wed Mar 11 2020 - 10:13:35 PDT)
Re: [AMBER] REMD hybrid solvent model
(Wed Mar 11 2020 - 08:35:21 PDT)
[AMBER] REMD hybrid solvent model
(Tue Mar 10 2020 - 13:09:00 PDT)
Hunter Wilson
Re: [AMBER] Writing Trajectories as netcdf files
(Wed Mar 25 2020 - 12:19:46 PDT)
[AMBER] Writing Trajectories as netcdf files
(Wed Mar 25 2020 - 10:11:08 PDT)
James Kress
Re: [AMBER] How to setup a QM/MM calculation in Amber
(Fri Mar 27 2020 - 11:57:17 PDT)
Re: [AMBER] Question of units
(Mon Mar 02 2020 - 18:47:26 PST)
[AMBER] Question of units
(Mon Mar 02 2020 - 14:19:12 PST)
Re: [AMBER] g09 genecp in QM/MM MD in amber
(Mon Mar 02 2020 - 11:22:30 PST)
Kellon Belfon
Re: [AMBER] Modified force fields
(Tue Mar 10 2020 - 10:48:50 PDT)
Re: [AMBER] Modified force fields
(Sun Mar 08 2020 - 15:23:08 PDT)
Kenneth Huang
Re: [AMBER] nastruct and modified base pairs
(Thu Mar 26 2020 - 17:47:02 PDT)
Re: [AMBER] nastruct and modified base pairs
(Wed Mar 25 2020 - 14:10:44 PDT)
[AMBER] nastruct and modified base pairs
(Wed Mar 25 2020 - 11:47:01 PDT)
Kosuke Tachibana
Re: [AMBER] Installation problem for a parallel version of Amber18/AmberTools19
(Wed Mar 25 2020 - 04:26:47 PDT)
Re: [AMBER] Installation problem for a parallel version of Amber18/AmberTools19
(Wed Mar 25 2020 - 02:57:54 PDT)
Re: [AMBER] Installation problem for a parallel version of Amber18/AmberTools19
(Tue Mar 24 2020 - 08:57:37 PDT)
[AMBER] Installation problem for a parallel version of Amber18/AmberTools19
(Sun Mar 22 2020 - 21:02:09 PDT)
koushik
Re: [AMBER] REMD hybrid solvent model
(Wed Mar 11 2020 - 10:35:51 PDT)
koushik kasavajhala
Re: [AMBER] EXTRACTING A PARTICULAR FRAME
(Thu Mar 12 2020 - 10:49:12 PDT)
Re: [AMBER] REMD hybrid solvent model
(Tue Mar 10 2020 - 13:24:06 PDT)
Lara rajam
[AMBER] Reg: MMGBSA for NAMD trajectory
(Wed Mar 11 2020 - 10:25:51 PDT)
Lenka
[AMBER] SImulation prepared using CHARMM GUI terminates with no error at the NTP step
(Wed Mar 25 2020 - 16:16:37 PDT)
Manish Manish
Re: [AMBER] CUDA single gpu usage issue
(Tue Mar 03 2020 - 21:54:16 PST)
Mariana Simoes Ferreira
[AMBER] AmberTools19 serial installation test errors
(Thu Mar 12 2020 - 12:57:39 PDT)
mark.bergman.uphs.upenn.edu
[AMBER] AmberTools19 update.8 fails to install
(Fri Mar 27 2020 - 14:49:04 PDT)
Matias Machado
Re: [AMBER] adding Na, K and Cl ions matching intracellular conc
(Fri Mar 06 2020 - 07:32:57 PST)
Re: [AMBER] adding Na, K and Cl ions matching intracellular conc
(Fri Mar 06 2020 - 07:29:54 PST)
Re: [AMBER] adding Na, K and Cl ions matching intracellular conc
(Wed Mar 04 2020 - 16:24:40 PST)
Re: [AMBER] adding Na, K and Cl ions matching intracellular conc
(Wed Mar 04 2020 - 16:23:01 PST)
Michael Shokhen
[AMBER] CUDA version for AMBER 16 and 20?
(Sun Mar 15 2020 - 10:56:00 PDT)
mirzo
Re: [AMBER] Error while amber installation
(Sat Mar 28 2020 - 21:57:58 PDT)
MYRIAN TORRES RICO
[AMBER] error job.sh
(Thu Mar 05 2020 - 09:05:40 PST)
Nicholas Moyer
Re: [AMBER] CUDA single gpu usage issue
(Fri Mar 06 2020 - 06:15:43 PST)
Re: [AMBER] CUDA single gpu usage issue
(Wed Mar 04 2020 - 08:24:59 PST)
Re: [AMBER] CUDA single gpu usage issue
(Tue Mar 03 2020 - 14:04:07 PST)
Re: [AMBER] CUDA single gpu usage issue
(Tue Mar 03 2020 - 10:21:56 PST)
Re: [AMBER] CUDA single gpu usage issue
(Tue Mar 03 2020 - 10:20:30 PST)
[AMBER] CUDA single gpu usage issue
(Tue Mar 03 2020 - 06:03:58 PST)
Nicolas Feldman
Re: [AMBER] checkstructure with cpptraj
(Tue Mar 31 2020 - 13:00:19 PDT)
Re: [AMBER] checkstructure with cpptraj
(Tue Mar 31 2020 - 12:58:17 PDT)
Re: [AMBER] checkstructure with cpptraj
(Tue Mar 31 2020 - 11:08:08 PDT)
Re: [AMBER] checkstructure with cpptraj
(Sun Mar 29 2020 - 16:18:02 PDT)
[AMBER] checkstructure with cpptraj
(Sun Mar 29 2020 - 08:26:34 PDT)
Re: [AMBER] setting pdb file
(Sat Mar 21 2020 - 10:03:59 PDT)
Re: [AMBER] setting pdb file
(Fri Mar 20 2020 - 15:57:24 PDT)
Re: [AMBER] setting pdb file
(Fri Mar 20 2020 - 15:44:02 PDT)
Re: [AMBER] setting pdb file
(Fri Mar 20 2020 - 13:01:15 PDT)
Re: [AMBER] setting pdb file
(Fri Mar 20 2020 - 12:41:57 PDT)
[AMBER] setting pdb file
(Fri Mar 20 2020 - 11:49:46 PDT)
[AMBER] problem adding MG.off file
(Mon Mar 02 2020 - 04:31:19 PST)
Oliver Grant
[AMBER] Ambmask Error in group input::atommask.f::pop_evalstack stack underflow
(Fri Mar 20 2020 - 02:35:20 PDT)
Osman, Roman
Re: [AMBER] PDB Modification
(Mon Mar 30 2020 - 09:08:00 PDT)
Re: [AMBER] PDB Modification
(Mon Mar 30 2020 - 08:30:39 PDT)
Pengfei Li
Re: [AMBER] "Error of reading the .dat file" in MCPB.py step 2
(Fri Mar 27 2020 - 15:14:19 PDT)
Re: [AMBER] KeyError: 'MG'
(Fri Mar 27 2020 - 14:26:40 PDT)
Re: [AMBER] KeyError: 'MG'
(Fri Mar 27 2020 - 14:21:21 PDT)
Re: [AMBER] problem in MCPB.py
(Fri Mar 27 2020 - 14:05:29 PDT)
Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial
(Fri Mar 27 2020 - 13:57:51 PDT)
Re: [AMBER] heme B parameter by mcpb
(Fri Mar 27 2020 - 13:54:42 PDT)
Petro
Re: [AMBER] how to turned off C N terminal amino in tleap
(Sun Mar 15 2020 - 02:51:19 PDT)
Re: [AMBER] GAFF/AMBER peptide bond
(Sat Mar 14 2020 - 15:16:45 PDT)
Re: [AMBER] GAFF/AMBER peptide bond
(Sat Mar 14 2020 - 14:43:35 PDT)
[AMBER] GAFF/AMBER peptide bond
(Sat Mar 14 2020 - 14:21:40 PDT)
[AMBER] Modified AA residue without NH2 end.
(Thu Mar 12 2020 - 03:41:16 PDT)
Prasanth G, Research Scholar
[AMBER] information regarding space filling visualization
(Sat Mar 14 2020 - 02:18:55 PDT)
Rakesh Srivastava
Re: [AMBER] Query regarding 3DRISM in Amber with CHARMM force field
(Fri Mar 06 2020 - 22:20:51 PST)
Raman Preet Singh
Re: [AMBER] AmberTools19 install error
(Mon Mar 09 2020 - 05:40:06 PDT)
Re: [AMBER] AmberTools19 install error
(Sun Mar 08 2020 - 10:59:22 PDT)
[AMBER] AmberTools19 install error
(Sun Mar 08 2020 - 07:03:00 PDT)
Ray Luo
Re: [AMBER] mmpbsa_py_energy failed with prmtop dim_gas.prmtop
(Fri Mar 27 2020 - 09:35:16 PDT)
Re: [AMBER] CUDA single gpu usage issue
(Thu Mar 05 2020 - 22:33:43 PST)
Re: [AMBER] CUDA single gpu usage issue
(Wed Mar 04 2020 - 10:03:55 PST)
Re: [AMBER] CUDA single gpu usage issue
(Tue Mar 03 2020 - 19:06:19 PST)
Re: [AMBER] CUDA single gpu usage issue
(Tue Mar 03 2020 - 10:26:35 PST)
Re: [AMBER] CUDA single gpu usage issue
(Tue Mar 03 2020 - 10:16:22 PST)
Rinsha Chk
Re: [AMBER] Question about MMPBSA calculation
(Mon Mar 09 2020 - 06:31:50 PDT)
[AMBER] Question about MMPBSA calculation
(Mon Mar 09 2020 - 03:06:13 PDT)
Robert Molt
Re: [AMBER] Abasic Site and Leap Polymerization
(Mon Mar 30 2020 - 10:08:06 PDT)
[AMBER] Abasic Site and Leap Polymerization
(Mon Mar 30 2020 - 07:35:44 PDT)
Robin Betz
Re: [AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results?
(Fri Mar 06 2020 - 13:08:21 PST)
Rodrigo Galindo-Murillo
Re: [AMBER] 2DRMS before clustering
(Sat Mar 07 2020 - 13:10:01 PST)
Rohit Zambre
[AMBER] MPI+threads in Amber
(Mon Mar 30 2020 - 10:01:21 PDT)
Rosellen, Martin
[AMBER] Error: Could not find angle parameter
(Sun Mar 29 2020 - 05:41:59 PDT)
Ross Walker
Re: [AMBER] Problems with Nvidia Drivers
(Sat Mar 28 2020 - 07:32:07 PDT)
Re: [AMBER] Problems with Nvidia Drivers
(Thu Mar 26 2020 - 12:49:14 PDT)
Ruxi Qi
Re: [AMBER] AMBER 18 compilation error with CUDA 10.2
(Wed Mar 04 2020 - 06:22:27 PST)
Re: [AMBER] CUDA single gpu usage issue
(Wed Mar 04 2020 - 01:22:42 PST)
Re: [AMBER] CUDA single gpu usage issue
(Wed Mar 04 2020 - 01:05:57 PST)
Sadaf Rani
Re: [AMBER] How to setup a QM/MM calculation in Amber
(Fri Mar 27 2020 - 17:55:11 PDT)
Re: [AMBER] How to setup a QM/MM calculation in Amber
(Fri Mar 27 2020 - 16:39:12 PDT)
[AMBER] How to setup a QM/MM calculation in Amber
(Fri Mar 27 2020 - 02:36:32 PDT)
Sasthi Mandal
[AMBER] Questions on force field
(Fri Mar 13 2020 - 00:03:28 PDT)
SATYAJIT KHATUA
Re: [AMBER] AMBER Digest, Vol 2934, Issue 1
(Thu Mar 12 2020 - 12:51:53 PDT)
[AMBER] Unavailability of the file related to -cprestrt flag in equilibration (NPT) step of constant pH MD in Amber14 with AmberTools15
(Fri Mar 06 2020 - 23:14:32 PST)
Serena Vittorio
[AMBER] GPU support information
(Tue Mar 24 2020 - 03:12:26 PDT)
SHAUNAK BADANI
[AMBER] Incosistency in energy values from out files and cpptraj energy tools
(Tue Mar 10 2020 - 08:20:02 PDT)
[AMBER] Inconsistency in energy values between out files and cpptraj
(Sat Mar 07 2020 - 03:56:38 PST)
[AMBER] Issue in drug parameter
(Sun Mar 01 2020 - 10:13:45 PST)
Siavoush Dastmalchi
[AMBER] What is the default pH when loading a protein in Amber environment
(Wed Mar 11 2020 - 04:20:41 PDT)
Song, Lin
Re: [AMBER] GAFF/AMBER peptide bond
(Sat Mar 14 2020 - 14:56:15 PDT)
Re: [AMBER] GAFF/AMBER peptide bond
(Sat Mar 14 2020 - 14:33:03 PDT)
Sruthi Sudhakar
[AMBER] unusual planarity change during md.
(Thu Mar 12 2020 - 08:25:40 PDT)
Re: [AMBER] EXTRACTING A PARTICULAR FRAME
(Thu Mar 12 2020 - 04:14:38 PDT)
Re: [AMBER] EXTRACTING A PARTICULAR FRAME
(Thu Mar 12 2020 - 01:12:32 PDT)
[AMBER] EXTRACTING A PARTICULAR FRAME
(Thu Mar 12 2020 - 00:41:28 PDT)
Re: [AMBER] Citing DNA OL15 forcefield
(Thu Mar 05 2020 - 01:00:18 PST)
[AMBER] Citing DNA OL15 forcefield
(Wed Mar 04 2020 - 11:14:40 PST)
Stephan Schott
Re: [AMBER] Writing Trajectories as netcdf files
(Wed Mar 25 2020 - 10:22:26 PDT)
Re: [AMBER] tleap for Mg2+ data type
(Wed Mar 25 2020 - 07:36:52 PDT)
Re: [AMBER] RTX 2020 Super GPU Random Memory Errors
(Sat Mar 21 2020 - 16:44:27 PDT)
SUNITA MUDULI
[AMBER] Amber restart simulation
(Tue Mar 31 2020 - 04:55:33 PDT)
Sunita Patel
Re: [AMBER] NPT equilibration is crashing
(Sun Mar 29 2020 - 03:37:43 PDT)
[AMBER] NPT equilibration is crashing
(Sat Mar 28 2020 - 21:11:36 PDT)
Re: [AMBER] tleap for Mg2+ data type
(Thu Mar 26 2020 - 20:26:25 PDT)
Re: [AMBER] tleap for Mg2+ data type
(Thu Mar 26 2020 - 20:19:21 PDT)
Re: [AMBER] tleap for Mg2+ data type
(Wed Mar 25 2020 - 17:32:05 PDT)
[AMBER] tleap for Mg2+ data type
(Wed Mar 25 2020 - 07:15:44 PDT)
Thomas Cheatham
Re: [AMBER] FATAL Error: Atom does not have a type (Cation)
(Wed Mar 25 2020 - 14:09:54 PDT)
Thomas Gaillard
[AMBER] about TREE_CHAIN_CLASSIFICATION
(Fri Mar 20 2020 - 05:16:40 PDT)
Tiejun Wei
[AMBER] Texas red force field
(Mon Mar 16 2020 - 08:27:20 PDT)
ttz
Re: [AMBER] questions about paramfit and frcmod file
(Mon Mar 23 2020 - 21:00:34 PDT)
[AMBER] questions about paramfit and frcmod file
(Sun Mar 22 2020 - 15:11:30 PDT)
Vaibhav Dixit
Re: [AMBER] adding Na, K and Cl ions matching intracellular conc
(Fri Mar 06 2020 - 07:50:09 PST)
Re: [AMBER] adding Na, K and Cl ions matching intracellular conc
(Wed Mar 04 2020 - 20:19:41 PST)
[AMBER] adding Na, K and Cl ions matching intracellular conc
(Wed Mar 04 2020 - 04:49:40 PST)
Re: [AMBER] g09 genecp in QM/MM MD in amber
(Mon Mar 02 2020 - 19:30:11 PST)
[AMBER] g09 genecp in QM/MM MD in amber
(Sun Mar 01 2020 - 19:48:01 PST)
Vishal Reddy
[AMBER] ** NFE-Error ** : Cannot read &colvar namelist!
(Mon Mar 23 2020 - 05:56:37 PDT)
[AMBER] Not recognising output file for N_OF_BONDS reaction coordinate
(Fri Mar 13 2020 - 12:07:31 PDT)
Vlad Cojocaru
Re: [AMBER] ff19SB + BSC1 + OPC + which ions ?
(Sun Mar 29 2020 - 08:27:36 PDT)
[AMBER] ff19SB + BSC1 + OPC + which ions ?
(Sun Mar 29 2020 - 05:36:41 PDT)
Re: [AMBER] simulations of proteins with 2 domains connected by a linker
(Thu Mar 12 2020 - 11:03:40 PDT)
[AMBER] simulations of proteins with 2 domains connected by a linker
(Thu Mar 12 2020 - 02:57:47 PDT)
wujue
[AMBER] problem in MCPB.py
(Wed Mar 04 2020 - 19:41:49 PST)
Yeng-Tseng Wang
Re: [AMBER] About the D form amino amber force field
(Sun Mar 15 2020 - 07:30:20 PDT)
[AMBER] About the D form amino amber force field
(Sun Mar 15 2020 - 01:53:07 PDT)
[AMBER] how to turned off C N terminal amino in tleap
(Sun Mar 15 2020 - 00:21:06 PDT)
Yoanes Vianney
Re: [AMBER] FATAL Error: Atom does not have a type (Cation)
(Wed Mar 25 2020 - 14:56:43 PDT)
[AMBER] FATAL Error: Atom does not have a type (Cation)
(Wed Mar 25 2020 - 13:28:33 PDT)
唐元晖
Re: [AMBER] A problem of "Could not import Amber Python modules"
(Wed Mar 18 2020 - 05:45:34 PDT)
[AMBER] A problem of "Could not import Amber Python modules"
(Tue Mar 17 2020 - 23:48:43 PDT)
杨明俊
Re: [AMBER] Lone Pairs in AMBER FF
(Thu Mar 19 2020 - 03:57:52 PDT)
Re: [AMBER] Lone Pairs in AMBER FF
(Sat Mar 14 2020 - 20:06:23 PDT)
[AMBER] Lone Pairs in AMBER FF
(Sat Mar 14 2020 - 07:35:18 PDT)
辛志宏
[AMBER] QM/MM Convergence questions
(Mon Mar 09 2020 - 20:02:03 PDT)
Re: [AMBER] QM/MM Convergence questions
(Mon Mar 09 2020 - 02:55:21 PDT)
Re: [AMBER] QM/MM Convergence questions
(Thu Mar 05 2020 - 18:22:32 PST)
[AMBER] QM/MM Convergence questions
(Thu Mar 05 2020 - 01:07:44 PST)
Last message date
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Tue Mar 31 2020 - 16:00:02 PDT
Archived on
: Wed Apr 24 2024 - 05:55:55 PDT
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