Amber Archive Sep 2017 by author
518 messages
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Starting
Fri Sep 01 2017 - 01:00:02 PDT,
Ending
Sat Sep 30 2017 - 06:00:03 PDT
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Aashish Bhatt
Re: [AMBER] Atom does not have file type -reg.
(Tue Sep 12 2017 - 08:51:37 PDT)
Re: [AMBER] Atom does not have file type -reg.
(Tue Sep 12 2017 - 08:09:33 PDT)
Re: [AMBER] Regarding Glucose naming
(Tue Sep 12 2017 - 08:00:12 PDT)
Re: [AMBER] Regarding Glucose naming
(Sun Sep 10 2017 - 00:57:44 PDT)
[AMBER] Regarding Glucose naming
(Sat Sep 09 2017 - 08:02:12 PDT)
ABEL Stephane
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
(Fri Sep 01 2017 - 07:23:54 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
(Fri Sep 01 2017 - 02:23:11 PDT)
Adrian Roitberg
Re: [AMBER] Avoid pH Titration of LYS and TYR
(Wed Sep 27 2017 - 12:48:29 PDT)
Re: [AMBER] Different production speeds at different pHs when doing explicit constant pH simulations
(Sun Sep 24 2017 - 09:15:45 PDT)
Re: [AMBER] cpinutil.py
(Thu Sep 21 2017 - 13:24:13 PDT)
Re: [AMBER] TI where charges change
(Thu Sep 14 2017 - 05:38:53 PDT)
Alessandro Mariani
[AMBER] Amber16 electric field parameters
(Thu Sep 21 2017 - 02:22:33 PDT)
Amani Eshtiwi
[AMBER] MCPB.py AmberTools17
(Thu Sep 21 2017 - 09:36:18 PDT)
Ana Luisa Novo de Oliveira
Re: [AMBER] simulations crash
(Fri Sep 22 2017 - 05:18:30 PDT)
[AMBER] simulations crash
(Fri Sep 22 2017 - 04:50:07 PDT)
Andreas Tosstorff
[AMBER] REMD one long or many short runs?
(Wed Sep 13 2017 - 06:18:02 PDT)
[AMBER] H++ salinity
(Fri Sep 01 2017 - 05:38:46 PDT)
Andrew Schaub
Re: [AMBER] Different production speeds at different pHs when doing explicit constant pH simulations
(Mon Sep 25 2017 - 14:52:49 PDT)
[AMBER] Different production speeds at different pHs when doing explicit constant pH simulations
(Sat Sep 23 2017 - 23:47:36 PDT)
Angus Voice
[AMBER] CpHMD and cys residues
(Mon Sep 18 2017 - 03:55:42 PDT)
Anhui Wang
[AMBER] How to use two different force fields for a molecule?
(Mon Sep 11 2017 - 07:09:05 PDT)
Ashutosh Shandilya
Re: [AMBER] Setting water box with fix dimension
(Thu Sep 21 2017 - 12:55:39 PDT)
[AMBER] Setting water box with fix dimension
(Thu Sep 21 2017 - 09:13:45 PDT)
Bartberger, Michael
Re: [AMBER] amberlite p38 tutorial: Failure of final step of "pymdpbsa" in amberlite
(Sat Sep 09 2017 - 14:57:41 PDT)
[AMBER] amberlite p38 tutorial: Failure of final step of "pymdpbsa" in amberlite
(Sun Sep 03 2017 - 09:25:31 PDT)
Battocchio, Giovanni
Re: [AMBER] gamd.log for multiple runs
(Wed Sep 13 2017 - 01:05:26 PDT)
[AMBER] gamd.log for multiple runs
(Mon Sep 11 2017 - 02:37:35 PDT)
Bill Ross
Re: [AMBER] Air-water interface
(Wed Sep 27 2017 - 09:58:25 PDT)
Re: [AMBER] Air-water interface
(Tue Sep 26 2017 - 23:03:46 PDT)
Re: [AMBER] cluster analysis using cpptraj
(Mon Sep 25 2017 - 03:00:38 PDT)
Re: [AMBER] cluster analysis using cpptraj
(Mon Sep 25 2017 - 02:30:48 PDT)
Re: [AMBER] cluster analysis using cpptraj
(Mon Sep 25 2017 - 02:29:18 PDT)
Re: [AMBER] cluster analysis using cpptraj
(Mon Sep 25 2017 - 02:28:23 PDT)
Re: [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command)
(Fri Sep 22 2017 - 08:07:12 PDT)
Re: [AMBER] SHAKE failure
(Fri Sep 22 2017 - 07:18:42 PDT)
Re: [AMBER] Setting water box with fix dimension
(Thu Sep 21 2017 - 13:00:01 PDT)
Re: [AMBER] Setting water box with fix dimension
(Thu Sep 21 2017 - 12:58:27 PDT)
Re: [AMBER] Problem with parallel install
(Thu Sep 21 2017 - 09:57:09 PDT)
Re: [AMBER] Problem with parallel install
(Wed Sep 20 2017 - 16:49:02 PDT)
Re: [AMBER] Problem with parallel install
(Wed Sep 20 2017 - 13:44:00 PDT)
Re: [AMBER] simulation of docked domains of protein
(Wed Sep 20 2017 - 12:49:30 PDT)
Re: [AMBER] Problem with parallel install
(Wed Sep 20 2017 - 12:33:18 PDT)
Re: [AMBER] Antechamber
(Wed Sep 20 2017 - 11:07:26 PDT)
Re: [AMBER] converting crd to pdb
(Tue Sep 19 2017 - 10:09:02 PDT)
Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion)
(Sun Sep 17 2017 - 00:04:23 PDT)
Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion)
(Sat Sep 16 2017 - 12:46:09 PDT)
Re: [AMBER] tleap atom numbering
(Mon Sep 11 2017 - 16:24:40 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 08:32:01 PDT)
Re: [AMBER] Atom does not have file type -reg.
(Mon Sep 11 2017 - 08:07:51 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 07:57:24 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 07:55:16 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 07:37:24 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 07:28:24 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 06:09:40 PDT)
Re: [AMBER] Frcmod file for ionic liquids
(Fri Sep 08 2017 - 12:22:46 PDT)
Re: [AMBER] Fixed links and files: Error in parmed: A residue defined as "fast 3-point water"...
(Thu Sep 07 2017 - 17:25:17 PDT)
Re: [AMBER] Error after using Parmed: A residue defined as "fast 3-point water"...
(Thu Sep 07 2017 - 16:23:39 PDT)
Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself
(Thu Sep 07 2017 - 01:11:27 PDT)
Re: [AMBER] Zinc dummy atom error in MMPBSA calculation
(Wed Sep 06 2017 - 10:05:06 PDT)
Re: [AMBER] Binding Free Energy Calculation in Ionic Liquid
(Sun Sep 03 2017 - 22:17:51 PDT)
Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
(Sun Sep 03 2017 - 18:17:29 PDT)
Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
(Sun Sep 03 2017 - 18:14:11 PDT)
Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
(Sun Sep 03 2017 - 18:11:50 PDT)
Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
(Fri Sep 01 2017 - 17:03:12 PDT)
Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
(Fri Sep 01 2017 - 17:01:45 PDT)
Carlos Simmerling
Re: [AMBER] leaprc.constph and ff14sb
(Thu Sep 28 2017 - 18:59:12 PDT)
Re: [AMBER] simulations crash
(Fri Sep 22 2017 - 05:48:16 PDT)
Re: [AMBER] simulations crash
(Fri Sep 22 2017 - 05:12:44 PDT)
Re: [AMBER] New Phospho Amino Acids Parameters?
(Fri Sep 15 2017 - 09:29:51 PDT)
Re: [AMBER] REMD one long or many short runs?
(Wed Sep 13 2017 - 06:37:28 PDT)
Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber
(Sat Sep 09 2017 - 04:16:12 PDT)
Re: [AMBER] umbrella sampling - restraint problem
(Fri Sep 08 2017 - 08:20:04 PDT)
Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber
(Fri Sep 08 2017 - 07:39:14 PDT)
[AMBER] Oct 2 deadline for awards applications, Computers in Chemistry Division of ACS
(Wed Sep 06 2017 - 05:27:12 PDT)
Re: [AMBER] ACE and NME capping protein is essential for protein simulation
(Fri Sep 01 2017 - 06:29:04 PDT)
Casalini Tommaso
Re: [AMBER] Amber16 archive corrupted?
(Wed Sep 13 2017 - 04:07:57 PDT)
[AMBER] Amber16 archive corrupted?
(Wed Sep 13 2017 - 03:30:01 PDT)
Celeste Saguí
Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested
(Thu Sep 21 2017 - 20:23:38 PDT)
Chayya Bhargac
Re: [AMBER] pmemd and sander simulations different - sander equilibration crashes
(Wed Sep 13 2017 - 09:30:11 PDT)
Re: [AMBER] pmemd and sander simulations different - sander equilibration crashes
(Wed Sep 13 2017 - 09:25:38 PDT)
Re: [AMBER] pmemd and sander simulations different - sander equilibration crashes
(Mon Sep 11 2017 - 10:51:32 PDT)
[AMBER] pmemd and sander simulations different - sander equilibration crashes
(Mon Sep 11 2017 - 09:34:14 PDT)
Chetna Tyagi
Re: [AMBER] Total energy of peptide simulation is positive
(Thu Sep 14 2017 - 08:31:06 PDT)
[AMBER] Total energy of peptide simulation is positive
(Thu Sep 14 2017 - 05:51:00 PDT)
Chris Neale
Re: [AMBER] simulation stop due to size limit exceed
(Thu Sep 21 2017 - 09:16:05 PDT)
Re: [AMBER] simulation time
(Tue Sep 19 2017 - 19:53:55 PDT)
Re: [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs
(Fri Sep 15 2017 - 11:09:34 PDT)
Re: [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs
(Tue Sep 12 2017 - 10:16:47 PDT)
[AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs
(Tue Sep 12 2017 - 09:28:30 PDT)
Chunli Yan
[AMBER] Split the image to run in the string method
(Thu Sep 21 2017 - 12:50:50 PDT)
colvin
[AMBER] rmsf < 5A
(Mon Sep 11 2017 - 01:11:46 PDT)
Cruzeiro,Vinicius Wilian D
Re: [AMBER] Explicit solvent CpHMD: seeking clarifications
(Sun Sep 03 2017 - 06:26:13 PDT)
D L S Dinuka
[AMBER] AmberTools 17 incomplete compilation
(Mon Sep 18 2017 - 05:31:04 PDT)
Daniel Mermelstein
Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber
(Wed Sep 13 2017 - 13:16:39 PDT)
Daniel Roe
Re: [AMBER] moveanchor
(Thu Sep 28 2017 - 09:13:24 PDT)
Re: [AMBER] RAC_analysis
(Thu Sep 28 2017 - 09:08:44 PDT)
Re: [AMBER] Cpptraj
(Thu Sep 28 2017 - 09:07:24 PDT)
Re: [AMBER] Problem with MM-GBSA decomposition
(Wed Sep 27 2017 - 10:22:47 PDT)
Re: [AMBER] Problem in analysing radius of gyration value in CPPTRAJ
(Wed Sep 27 2017 - 06:00:24 PDT)
Re: [AMBER] cpptraj distance: error
(Tue Sep 26 2017 - 10:10:40 PDT)
Re: [AMBER] cpptraj distance: error
(Tue Sep 26 2017 - 09:46:05 PDT)
Re: [AMBER] cluster analysis using cpptraj
(Mon Sep 25 2017 - 05:42:29 PDT)
Re: [AMBER] mdcrd file not open in vmd
(Fri Sep 22 2017 - 11:04:27 PDT)
Re: [AMBER] cluster analysis of protein complex simulation
(Fri Sep 22 2017 - 09:36:12 PDT)
Re: [AMBER] SHAKE failure
(Fri Sep 22 2017 - 07:08:39 PDT)
Re: [AMBER] simulations crash
(Fri Sep 22 2017 - 07:03:02 PDT)
Re: [AMBER] [david.case.rutgers.edu: Re: Is it possible to compile without linking C++ and fortran?]
(Fri Sep 22 2017 - 06:59:31 PDT)
Re: [AMBER] Is it possible to compile without linking C++ and fortran?
(Thu Sep 21 2017 - 17:07:21 PDT)
Re: [AMBER] Setting water box with fix dimension
(Thu Sep 21 2017 - 12:58:59 PDT)
Re: [AMBER] Setting water box with fix dimension
(Thu Sep 21 2017 - 12:46:09 PDT)
Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested
(Thu Sep 21 2017 - 12:43:10 PDT)
Re: [AMBER] Pytraj Gyration Tensor
(Thu Sep 21 2017 - 12:35:56 PDT)
Re: [AMBER] Is it possible to compile without linking C++ and fortran?
(Thu Sep 21 2017 - 12:26:29 PDT)
Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested
(Thu Sep 21 2017 - 08:53:44 PDT)
Re: [AMBER] Problem with parallel install
(Thu Sep 21 2017 - 08:01:37 PDT)
Re: [AMBER] cpptraj volmap: some questions
(Wed Sep 20 2017 - 09:26:59 PDT)
Re: [AMBER] Protein drifts out of the periodic cell
(Wed Sep 20 2017 - 08:56:16 PDT)
Re: [AMBER] Protein drifts out of the periodic cell
(Wed Sep 20 2017 - 05:35:22 PDT)
Re: [AMBER] Restart Simulation
(Tue Sep 19 2017 - 11:39:45 PDT)
Re: [AMBER] Problem with parallel install
(Tue Sep 19 2017 - 10:26:06 PDT)
Re: [AMBER] angle between two subdomains
(Tue Sep 19 2017 - 07:44:44 PDT)
Re: [AMBER] Problem with parallel install
(Tue Sep 19 2017 - 07:42:47 PDT)
Re: [AMBER] cpptraj: modification of topologies/trajectories
(Mon Sep 18 2017 - 12:23:03 PDT)
Re: [AMBER] cpptraj: usage of strip and parmstrip
(Mon Sep 18 2017 - 11:38:18 PDT)
Re: [AMBER] How to calculate RDF with 'radial'
(Mon Sep 18 2017 - 11:22:15 PDT)
Re: [AMBER] Is geometric center of atoms same as center of mass ?
(Mon Sep 18 2017 - 11:11:21 PDT)
Re: [AMBER] cpptraj: modification of topologies/trajectories
(Mon Sep 18 2017 - 06:01:14 PDT)
Re: [AMBER] AmberTools 17 incomplete compilation
(Mon Sep 18 2017 - 05:41:02 PDT)
Re: [AMBER] cpptraj: modification of topologies/trajectories
(Mon Sep 18 2017 - 05:38:21 PDT)
Re: [AMBER] Is geometric center of atoms same as center of mass ?
(Sat Sep 16 2017 - 04:46:09 PDT)
Re: [AMBER] cpptraj SPAM error
(Thu Sep 14 2017 - 09:34:56 PDT)
Re: [AMBER] cpptraj SPAM error
(Thu Sep 14 2017 - 08:49:37 PDT)
Re: [AMBER] cpptraj SPAM error
(Thu Sep 14 2017 - 08:16:55 PDT)
Re: [AMBER] How to calculate RDF with 'radial'
(Wed Sep 13 2017 - 06:39:48 PDT)
Re: [AMBER] Error in quasiharmonic calculation: prmtop file?
(Mon Sep 11 2017 - 09:07:38 PDT)
Re: [AMBER] rmsf < 5A
(Mon Sep 11 2017 - 06:07:34 PDT)
Re: [AMBER] umbrella sampling - restraint problem
(Mon Sep 11 2017 - 06:04:06 PDT)
Re: [AMBER] Problem in restarting pH-REMD CpHMD
(Fri Sep 08 2017 - 11:09:08 PDT)
Re: [AMBER] .crd file format error
(Tue Sep 05 2017 - 08:46:41 PDT)
Re: [AMBER] Cpptraj and parmwrite and strip
(Fri Sep 01 2017 - 13:27:18 PDT)
Re: [AMBER] Cpptraj and parmwrite and strip
(Fri Sep 01 2017 - 12:05:44 PDT)
Re: [AMBER] Calculation the Area per lipids using cpptraj
(Fri Sep 01 2017 - 06:13:58 PDT)
Re: [AMBER] significance of iwrap
(Fri Sep 01 2017 - 05:22:06 PDT)
Darrin York
[AMBER] GPU-accelerated thermodynamic integration available in Amber
(Tue Sep 12 2017 - 06:01:40 PDT)
David A Case
Re: [AMBER] How to save reimaged trajectory file during MD?
(Tue Sep 26 2017 - 10:17:15 PDT)
Re: [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command)
(Sat Sep 23 2017 - 14:30:19 PDT)
[AMBER] [david.case.rutgers.edu: Re: Is it possible to compile without linking C++ and fortran?]
(Thu Sep 21 2017 - 13:46:29 PDT)
Re: [AMBER] Setting water box with fix dimension
(Thu Sep 21 2017 - 13:30:33 PDT)
Re: [AMBER] Antechamber
(Thu Sep 21 2017 - 13:20:32 PDT)
Re: [AMBER] simulation of docked domains of protein
(Thu Sep 21 2017 - 13:16:55 PDT)
Re: [AMBER] ambertools install issue (Eric Smoll)
(Wed Sep 20 2017 - 08:21:49 PDT)
Re: [AMBER] How tleap read a Ruthenium complex solvent box generated by packmol?
(Tue Sep 19 2017 - 02:39:54 PDT)
Re: [AMBER] Problem with parallel install
(Mon Sep 18 2017 - 13:33:30 PDT)
Re: [AMBER] Manually set residues Protonation states for HIS and CYS
(Mon Sep 18 2017 - 08:19:11 PDT)
Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion)
(Sun Sep 17 2017 - 09:25:44 PDT)
Re: [AMBER] Installing Compiling Errors
(Thu Sep 14 2017 - 17:58:07 PDT)
Re: [AMBER] Total energy of peptide simulation is positive
(Thu Sep 14 2017 - 08:11:57 PDT)
Re: [AMBER] TI where charges change
(Thu Sep 14 2017 - 08:05:13 PDT)
Re: [AMBER] Deprotonated SER side residue by AMBER?
(Thu Sep 14 2017 - 05:02:06 PDT)
[AMBER] TI where charges change
(Thu Sep 14 2017 - 04:51:26 PDT)
Re: [AMBER] tleap error
(Wed Sep 13 2017 - 06:27:46 PDT)
Re: [AMBER] pmemd and sander simulations different - sander equilibration crashes
(Tue Sep 12 2017 - 04:25:07 PDT)
Re: [AMBER] Atom does not have file type -reg.
(Tue Sep 12 2017 - 04:21:04 PDT)
Re: [AMBER] How to use two different force fields for a molecule?
(Tue Sep 12 2017 - 04:16:11 PDT)
Re: [AMBER] Obtaining AM1-BCC charges in Antechamber
(Mon Sep 11 2017 - 05:19:18 PDT)
Re: [AMBER] tleap atom numbering
(Mon Sep 11 2017 - 05:07:13 PDT)
Re: [AMBER] index error -reg
(Sun Sep 10 2017 - 08:15:04 PDT)
Re: [AMBER] MD terminate in HPC
(Wed Sep 06 2017 - 05:43:06 PDT)
Re: [AMBER] Binding Free Energy Calculation in Ionic Liquid
(Mon Sep 04 2017 - 05:39:56 PDT)
Re: [AMBER] amberlite p38 tutorial: Failure of final step of "pymdpbsa" in amberlite
(Sun Sep 03 2017 - 18:27:21 PDT)
Re: [AMBER] ACE and NME capping protein is essential for protein simulation
(Fri Sep 01 2017 - 05:42:20 PDT)
David Adrian Saez San Martin
Re: [AMBER] Fixed links and files: Error in parmed: A residue defined as "fast 3-point water"...
(Fri Sep 08 2017 - 12:58:25 PDT)
Re: [AMBER] I only receive a digest, but not specific answers to my posts
(Fri Sep 08 2017 - 12:49:26 PDT)
[AMBER] I only receive a digest, but not specific answers to my posts
(Fri Sep 08 2017 - 12:36:40 PDT)
Re: [AMBER] Fixed links and files: Error in parmed: A residue defined as "fast 3-point water"...
(Fri Sep 08 2017 - 12:31:39 PDT)
[AMBER] Fixed links and files: Error in parmed: A residue defined as "fast 3-point water"...
(Thu Sep 07 2017 - 17:14:24 PDT)
David Cerutti
Re: [AMBER] NEW machine need help with GPU choice.
(Mon Sep 11 2017 - 19:25:06 PDT)
David Sáez
Re: [AMBER] Problem regarding Chamber and psf file
(Thu Sep 21 2017 - 21:30:22 PDT)
Re: [AMBER] Problem regarding Chamber and psf file
(Thu Sep 21 2017 - 13:45:09 PDT)
[AMBER] Error in pmemd.cuda
(Tue Sep 19 2017 - 22:58:39 PDT)
[AMBER] Error after using Parmed: A residue defined as "fast 3-point water"...
(Thu Sep 07 2017 - 16:07:32 PDT)
Debasish Mandal
[AMBER] Binding Free Energy Calculation in Ionic Liquid
(Sun Sep 03 2017 - 21:57:09 PDT)
diego.soler.uam.es
Re: [AMBER] umbrella sampling - restraint problem
(Fri Sep 08 2017 - 05:50:17 PDT)
Domenico Marson
Re: [AMBER] Pytraj Gyration Tensor
(Thu Sep 21 2017 - 10:08:04 PDT)
Re: [AMBER] Pytraj Gyration Tensor
(Thu Sep 21 2017 - 06:32:28 PDT)
Re: [AMBER] Pytraj Gyration Tensor
(Thu Sep 21 2017 - 04:29:54 PDT)
[AMBER] Pytraj Gyration Tensor
(Tue Sep 19 2017 - 03:18:19 PDT)
Dwight McGee
Re: [AMBER] MMPBSA.py failing with topologies
(Wed Sep 13 2017 - 22:29:16 PDT)
Elisa Pieri
Re: [AMBER] Problem in restarting pH-REMD CpHMD
(Sat Sep 09 2017 - 01:14:12 PDT)
[AMBER] Problem in restarting pH-REMD CpHMD
(Fri Sep 08 2017 - 05:43:56 PDT)
Elvis Martis
Re: [AMBER] Error with MMGBSA/PBSA
(Thu Sep 28 2017 - 12:21:52 PDT)
Re: [AMBER] Error with MMGBSA/PBSA
(Wed Sep 27 2017 - 09:53:44 PDT)
Re: [AMBER] Error with MMGBSA/PBSA
(Wed Sep 27 2017 - 09:28:17 PDT)
Re: [AMBER] How to save reimaged trajectory file during MD?
(Tue Sep 26 2017 - 00:37:11 PDT)
Re: [AMBER] cluster analysis using cpptraj
(Mon Sep 25 2017 - 06:38:10 PDT)
Re: [AMBER] Antechamber error
(Thu Sep 21 2017 - 07:39:14 PDT)
Re: [AMBER] simulation of docked domains of protein
(Wed Sep 20 2017 - 23:03:05 PDT)
Re: [AMBER] simulation of docked domains of protein
(Wed Sep 20 2017 - 09:36:07 PDT)
Re: [AMBER] simulation time
(Sat Sep 16 2017 - 20:22:16 PDT)
Re: [AMBER] simulation time
(Sat Sep 16 2017 - 11:34:34 PDT)
Re: [AMBER] simulation time
(Sat Sep 16 2017 - 11:14:40 PDT)
Re: [AMBER] Amber16 archive corrupted?
(Wed Sep 13 2017 - 04:05:47 PDT)
Re: [AMBER] Regarding Glucose naming
(Sat Sep 09 2017 - 20:06:26 PDT)
Re: [AMBER] MD terminate in HPC
(Wed Sep 06 2017 - 05:42:58 PDT)
Re: [AMBER] Residue wise energy decomposition via MM-PBSA
(Tue Sep 05 2017 - 23:37:16 PDT)
Eric Lang
Re: [AMBER] CpHMD: seeking clarification
(Mon Sep 25 2017 - 03:29:50 PDT)
Eric Pettersen
Re: [AMBER] Dr. Nick Riviera
(Wed Sep 27 2017 - 13:29:13 PDT)
Re: [AMBER] Dr. Nick Riviera
(Wed Sep 27 2017 - 12:49:31 PDT)
[AMBER] Dr. Nick Riviera
(Wed Sep 27 2017 - 12:43:21 PDT)
Eric Smoll
Re: [AMBER] ambertools install issue (Eric Smoll)
(Tue Sep 19 2017 - 12:38:21 PDT)
[AMBER] ambertools install issue
(Tue Sep 19 2017 - 10:50:30 PDT)
Feng Pan
Re: [AMBER] Split the image to run in the string method
(Thu Sep 21 2017 - 15:06:13 PDT)
Fábio Jorge
[AMBER] Error bad atom Br
(Sun Sep 03 2017 - 12:43:58 PDT)
Garima Singh
[AMBER] MD terminate in HPC
(Wed Sep 06 2017 - 03:49:05 PDT)
George Tzotzos
Re: [AMBER] cpptraj distance: error
(Tue Sep 26 2017 - 10:02:45 PDT)
[AMBER] cpptraj distance: error
(Tue Sep 26 2017 - 09:41:37 PDT)
Re: [AMBER] CpHMD: seeking clarification
(Mon Sep 25 2017 - 07:36:01 PDT)
[AMBER] CpHMD: seeking clarification
(Sun Sep 24 2017 - 10:41:05 PDT)
Re: [AMBER] cpptraj volmap: some questions
(Wed Sep 20 2017 - 11:36:05 PDT)
[AMBER] cpptraj: usage of strip and parmstrip
(Mon Sep 18 2017 - 11:15:45 PDT)
Re: [AMBER] cpptraj: modification of topologies/trajectories
(Mon Sep 18 2017 - 06:04:24 PDT)
Re: [AMBER] cpptraj: modification of topologies/trajectories
(Mon Sep 18 2017 - 05:53:02 PDT)
[AMBER] cpptraj: modification of topologies/trajectories
(Sun Sep 17 2017 - 08:02:43 PDT)
[AMBER] cpptraj volmap: some questions
(Fri Sep 15 2017 - 06:54:25 PDT)
Re: [AMBER] cpptraj SPAM error
(Thu Sep 14 2017 - 09:42:20 PDT)
Re: [AMBER] cpptraj SPAM error
(Thu Sep 14 2017 - 09:04:09 PDT)
Re: [AMBER] cpptraj SPAM error
(Thu Sep 14 2017 - 08:33:07 PDT)
Re: [AMBER] cpptraj SPAM error
(Thu Sep 14 2017 - 08:30:48 PDT)
[AMBER] cpptraj SPAM error
(Thu Sep 14 2017 - 08:13:50 PDT)
Re: [AMBER] Explicit solvent CpHMD: seeking clarifications
(Mon Sep 04 2017 - 04:09:30 PDT)
Re: [AMBER] Explicit solvent CpHMD: seeking clarifications
(Mon Sep 04 2017 - 08:56:36 PDT)
Re: [AMBER] Explicit solvent CpHMD: seeking clarifications
(Sun Sep 03 2017 - 04:57:44 PDT)
[AMBER] Explicit solvent CpHMD: seeking clarifications
(Sat Sep 02 2017 - 10:07:21 PDT)
guptashilpa_91.yahoo.com
[AMBER] Frcmod file for ionic liquids
(Fri Sep 08 2017 - 07:42:13 PDT)
Guqin Shi
Re: [AMBER] Question about MM/PBSA idecomp=1: decomposed Eelec stays the same when internal dielec constant increases. Is this a bug?
(Tue Sep 05 2017 - 08:54:40 PDT)
[AMBER] Question about MM/PBSA idecomp=1: Eelec from receptor and ligand don't add up
(Mon Sep 04 2017 - 17:13:25 PDT)
Hadházi Ádám
Re: [AMBER] TI where charges change
(Thu Sep 14 2017 - 10:44:15 PDT)
Re: [AMBER] TI where charges change
(Thu Sep 14 2017 - 06:10:46 PDT)
Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber
(Wed Sep 13 2017 - 14:33:30 PDT)
Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber
(Wed Sep 13 2017 - 11:33:49 PDT)
Hai Nguyen
Re: [AMBER] trajout last x frames cpptraj
(Thu Sep 28 2017 - 20:28:55 PDT)
Re: [AMBER] trajout last x frames cpptraj
(Thu Sep 28 2017 - 20:27:32 PDT)
Re: [AMBER] Problem in analysing radius of gyration value in CPPTRAJ
(Wed Sep 27 2017 - 06:21:30 PDT)
Re: [AMBER] cpinutil.py
(Mon Sep 25 2017 - 10:57:46 PDT)
Re: [AMBER] cluster analysis of protein complex simulation
(Fri Sep 22 2017 - 09:13:03 PDT)
Re: [AMBER] Pytraj Gyration Tensor
(Thu Sep 21 2017 - 21:43:16 PDT)
Re: [AMBER] cpinutil.py
(Thu Sep 21 2017 - 21:40:38 PDT)
Re: [AMBER] Pytraj Gyration Tensor
(Thu Sep 21 2017 - 12:38:32 PDT)
Re: [AMBER] Pytraj Gyration Tensor
(Thu Sep 21 2017 - 10:28:13 PDT)
Re: [AMBER] Question about MCPB.py
(Thu Sep 21 2017 - 09:49:12 PDT)
Re: [AMBER] Pytraj Gyration Tensor
(Thu Sep 21 2017 - 05:33:22 PDT)
Re: [AMBER] ambertools install issue (Eric Smoll)
(Tue Sep 19 2017 - 14:11:12 PDT)
Re: [AMBER] ambertools install issue
(Tue Sep 19 2017 - 11:07:04 PDT)
Re: [AMBER] converting crd to pdb
(Tue Sep 19 2017 - 10:11:45 PDT)
Re: [AMBER] Pytraj Gyration Tensor
(Tue Sep 19 2017 - 05:49:25 PDT)
Re: [AMBER] AmberTools 17 incomplete compilation
(Mon Sep 18 2017 - 15:19:58 PDT)
Re: [AMBER] simulation time
(Sat Sep 16 2017 - 11:39:04 PDT)
Re: [AMBER] Installing Compiling Errors
(Thu Sep 14 2017 - 13:39:30 PDT)
Re: [AMBER] Creation of unusual bonding via pdb4amber.
(Tue Sep 12 2017 - 21:16:50 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 19:58:04 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 19:49:03 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 19:48:50 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 19:43:50 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 19:39:10 PDT)
Re: [AMBER] Creation of unusual bonding via pdb4amber.
(Tue Sep 12 2017 - 19:36:38 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 19:18:03 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 19:10:26 PDT)
Re: [AMBER] Creation of unusual bonding via pdb4amber.
(Tue Sep 12 2017 - 18:37:39 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 05:57:25 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 05:45:00 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 05:25:30 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Mon Sep 11 2017 - 21:39:44 PDT)
Re: [AMBER] How to use two different force fields for a molecule?
(Mon Sep 11 2017 - 09:09:51 PDT)
Re: [AMBER] Error in quasiharmonic calculation: prmtop file?
(Sat Sep 09 2017 - 19:52:44 PDT)
Hector A. Baldoni
Re: [AMBER] Regarding Glucose naming
(Sun Sep 10 2017 - 11:02:38 PDT)
hongping zhang
[AMBER] CNT
(Sun Sep 10 2017 - 18:58:34 PDT)
Hughes, Travis
Re: [AMBER] trajout last x frames cpptraj
(Fri Sep 29 2017 - 07:34:35 PDT)
[AMBER] trajout last x frames cpptraj
(Thu Sep 28 2017 - 11:23:06 PDT)
Istvan Kolossvary
[AMBER] Inverting a selection in NAB atom expression?
(Wed Sep 20 2017 - 13:47:52 PDT)
jacky zhao
[AMBER] RAC_analysis
(Thu Sep 28 2017 - 06:53:27 PDT)
[AMBER] How to compare the difference between two trajectories with two very similar parm files
(Fri Sep 22 2017 - 18:32:12 PDT)
Re: [AMBER] cluster analysis of protein complex simulation
(Fri Sep 22 2017 - 18:22:43 PDT)
[AMBER] cluster analysis of protein complex simulation
(Fri Sep 22 2017 - 08:10:09 PDT)
Re: [AMBER] tleap error
(Wed Sep 13 2017 - 06:48:03 PDT)
Re: [AMBER] tleap error
(Wed Sep 13 2017 - 05:15:56 PDT)
Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber
(Wed Sep 13 2017 - 05:13:13 PDT)
[AMBER] tleap error
(Wed Sep 13 2017 - 03:28:24 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 20:06:00 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 19:52:44 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 19:45:30 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 19:36:23 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 18:52:04 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 05:55:21 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 05:54:12 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 05:39:23 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 05:31:26 PDT)
Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Tue Sep 12 2017 - 02:07:28 PDT)
[AMBER] Could not import Amber Python modules when using mdout_analyzer.py
(Mon Sep 11 2017 - 21:31:50 PDT)
Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber
(Sat Sep 09 2017 - 00:25:57 PDT)
Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber
(Fri Sep 08 2017 - 07:28:56 PDT)
[AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber
(Mon Sep 04 2017 - 22:00:53 PDT)
[AMBER] Missing amino acids preparation for long-term simulation
(Fri Sep 01 2017 - 09:31:43 PDT)
Re: [AMBER] ACE and NME capping protein is essential for protein simulation
(Fri Sep 01 2017 - 08:55:56 PDT)
Re: [AMBER] ACE and NME capping protein is essential for protein simulation
(Fri Sep 01 2017 - 08:50:19 PDT)
[AMBER] ACE and NME capping protein is essential for protein simulation
(Fri Sep 01 2017 - 03:30:57 PDT)
jacob wick
Re: [AMBER] Error with MMGBSA/PBSA
(Thu Sep 28 2017 - 07:01:01 PDT)
Re: [AMBER] Error with MMGBSA/PBSA
(Wed Sep 27 2017 - 09:34:06 PDT)
[AMBER] Error with MMGBSA/PBSA
(Wed Sep 27 2017 - 08:38:17 PDT)
James Kress
Re: [AMBER] Error bad atom Br
(Sun Sep 03 2017 - 16:35:42 PDT)
James Starlight
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
(Fri Sep 01 2017 - 06:08:35 PDT)
Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui
(Fri Sep 01 2017 - 00:52:56 PDT)
Jason Swails
Re: [AMBER] Different production speeds at different pHs when doing explicit constant pH simulations
(Tue Sep 26 2017 - 12:27:06 PDT)
Re: [AMBER] Problem regarding Chamber and psf file
(Thu Sep 21 2017 - 20:16:41 PDT)
Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber
(Wed Sep 13 2017 - 19:52:00 PDT)
Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself
(Sat Sep 09 2017 - 19:18:54 PDT)
Re: [AMBER] Explicit solvent CpHMD: seeking clarifications
(Sun Sep 03 2017 - 04:42:40 PDT)
jesus berlanga
Re: [AMBER] Air-water interface
(Wed Sep 27 2017 - 09:44:32 PDT)
[AMBER] Air-water interface
(Tue Sep 26 2017 - 22:58:12 PDT)
Jeyaram R A
Re: [AMBER] Atom does not have file type -reg.
(Tue Sep 12 2017 - 08:34:02 PDT)
Re: [AMBER] Atom does not have file type -reg.
(Tue Sep 12 2017 - 07:21:01 PDT)
[AMBER] Atom does not have file type -reg.
(Mon Sep 11 2017 - 08:04:39 PDT)
[AMBER] index error -reg
(Sun Sep 10 2017 - 04:54:00 PDT)
Kanin Wichapong
[AMBER] protein-membrane visualize in VMD
(Wed Sep 20 2017 - 09:00:05 PDT)
Khabiri, Morteza
Re: [AMBER] Cpptraj and parmwrite and strip
(Fri Sep 01 2017 - 12:44:20 PDT)
Re: [AMBER] Cpptraj and parmwrite and strip
(Fri Sep 01 2017 - 12:37:58 PDT)
[AMBER] Cpptraj and parmwrite and strip
(Fri Sep 01 2017 - 11:16:16 PDT)
krishna.2015.iitg.ernet.in
Re: [AMBER] Problem in analysing radius of gyration value in CPPTRAJ
(Thu Sep 28 2017 - 04:01:40 PDT)
[AMBER] [Fwd: Re: Problem in analysing radius of gyration value in CPPTRAJ]
(Wed Sep 27 2017 - 11:35:23 PDT)
[AMBER] Problem in analysing radius of gyration value in CPPTRAJ
(Tue Sep 26 2017 - 09:07:04 PDT)
Lizelle Lubbe
Re: [AMBER] SHAKE failure
(Tue Sep 26 2017 - 06:14:46 PDT)
Re: [AMBER] SHAKE failure
(Tue Sep 26 2017 - 05:56:35 PDT)
Re: [AMBER] SHAKE failure
(Tue Sep 26 2017 - 03:34:12 PDT)
Re: [AMBER] SHAKE failure
(Fri Sep 22 2017 - 11:40:36 PDT)
Re: [AMBER] SHAKE failure
(Fri Sep 22 2017 - 11:37:05 PDT)
[AMBER] SHAKE failure
(Fri Sep 22 2017 - 05:30:13 PDT)
[AMBER] Distance restraint
(Wed Sep 20 2017 - 07:26:44 PDT)
Re: [AMBER] improper torsion terms
(Wed Sep 20 2017 - 00:57:16 PDT)
[AMBER] improper torsion terms
(Mon Sep 18 2017 - 09:07:08 PDT)
Re: [AMBER] Minimization error due to modified residue
(Tue Sep 12 2017 - 07:43:13 PDT)
Re: [AMBER] Minimization error due to modified residue
(Tue Sep 12 2017 - 05:05:32 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 08:43:07 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 07:59:38 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 07:48:26 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 07:30:29 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 07:21:05 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 07:03:57 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 06:12:46 PDT)
Lê Ngọc Chính
Re: [AMBER] Question about MCPB.py
(Thu Sep 21 2017 - 09:57:27 PDT)
[AMBER] Question about MCPB.py
(Thu Sep 21 2017 - 09:26:05 PDT)
[AMBER] Question about MCPB.py
(Thu Sep 21 2017 - 00:07:33 PDT)
Re: [AMBER] Moldeling with MCPB.py
(Sun Sep 10 2017 - 09:22:02 PDT)
[AMBER] Moldeling with MCPB.py
(Mon Sep 04 2017 - 04:09:45 PDT)
Mandar Kulkarni
[AMBER] Hoogsteen base pair using "useboundsfrom"
(Tue Sep 19 2017 - 02:42:05 PDT)
Maria Clelia Milletti
Re: [AMBER] Problem with parallel install
(Thu Sep 21 2017 - 10:35:45 PDT)
Re: [AMBER] Problem with parallel install
(Thu Sep 21 2017 - 06:54:18 PDT)
Re: [AMBER] Problem with parallel install
(Wed Sep 20 2017 - 13:54:28 PDT)
Re: [AMBER] Problem with parallel install
(Wed Sep 20 2017 - 13:13:55 PDT)
Re: [AMBER] Problem with parallel install
(Wed Sep 20 2017 - 12:30:25 PDT)
Re: [AMBER] Problem with parallel install
(Tue Sep 19 2017 - 08:53:20 PDT)
Re: [AMBER] Problem with parallel install
(Tue Sep 19 2017 - 07:35:58 PDT)
[AMBER] Problem with parallel install
(Mon Sep 18 2017 - 09:18:47 PDT)
martin.lepsik.uochb.cas.cz
[AMBER] New Phospho Amino Acids Parameters?
(Fri Sep 15 2017 - 01:32:46 PDT)
Michael Shokhen
Re: [AMBER] Protein drifts out of the periodic cell
(Wed Sep 20 2017 - 09:03:24 PDT)
Re: [AMBER] Protein drifts out of the periodic cell
(Wed Sep 20 2017 - 08:35:22 PDT)
[AMBER] Protein drifts out of the periodic cell
(Wed Sep 20 2017 - 02:21:07 PDT)
Re: [AMBER] Deprotonated SER side residue by AMBER?
(Thu Sep 14 2017 - 06:25:52 PDT)
[AMBER] Deprotonated SER side residue by AMBER?
(Wed Sep 13 2017 - 10:18:07 PDT)
[AMBER] TLEAP generation of ionized amino acid residue?
(Mon Sep 11 2017 - 03:38:55 PDT)
Mo Rahman
Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested
(Thu Sep 21 2017 - 13:15:56 PDT)
Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested
(Thu Sep 21 2017 - 10:16:43 PDT)
[AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested
(Thu Sep 21 2017 - 08:36:55 PDT)
Mohit Mazumder
[AMBER] NEW machine need help with GPU choice.
(Mon Sep 11 2017 - 18:46:02 PDT)
Nada Afiva
Re: [AMBER] Error in quasiharmonic calculation: prmtop file?
(Sat Sep 09 2017 - 20:55:07 PDT)
[AMBER] Error in quasiharmonic calculation: prmtop file?
(Sat Sep 09 2017 - 19:50:48 PDT)
Neha Gandhi
Re: [AMBER] tleap atom numbering
(Mon Sep 11 2017 - 14:38:23 PDT)
[AMBER] tleap atom numbering
(Sun Sep 10 2017 - 18:38:03 PDT)
Niel Henriksen
Re: [AMBER] Dr. Nick Riviera
(Wed Sep 27 2017 - 13:20:07 PDT)
Nisha Amarnath Jonniya
Re: [AMBER] umbrella sampling - restraint problem
(Sun Sep 10 2017 - 22:21:44 PDT)
Re: [AMBER] umbrella sampling - restraint problem
(Fri Sep 08 2017 - 07:57:10 PDT)
[AMBER] umbrella sampling - restraint problem
(Fri Sep 08 2017 - 04:37:14 PDT)
Pacheco, Sayuri
Re: [AMBER] Cpptraj
(Thu Sep 28 2017 - 14:59:02 PDT)
Re: [AMBER] Cpptraj
(Thu Sep 28 2017 - 14:52:09 PDT)
Re: [AMBER] cpinutil.py
(Mon Sep 25 2017 - 10:47:39 PDT)
Re: [AMBER] cpinutil.py
(Thu Sep 21 2017 - 13:56:31 PDT)
[AMBER] cpinutil.py
(Thu Sep 21 2017 - 12:45:40 PDT)
pancham lal Gupta
Re: [AMBER] water bridge analysis
(Mon Sep 25 2017 - 17:22:09 PDT)
Re: [AMBER] .com file creation
(Tue Sep 19 2017 - 17:30:49 PDT)
Parviz Seifpanahi Shabane
Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
(Sun Sep 03 2017 - 18:19:56 PDT)
Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
(Sun Sep 03 2017 - 18:15:32 PDT)
Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
(Sun Sep 03 2017 - 18:12:55 PDT)
Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
(Sun Sep 03 2017 - 18:10:13 PDT)
Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
(Fri Sep 01 2017 - 16:57:38 PDT)
Pengfei Li
Re: [AMBER] Amber16 electric field parameters
(Sat Sep 23 2017 - 15:35:06 PDT)
Re: [AMBER] Antechamber RESP calculation error
(Sat Sep 23 2017 - 15:31:57 PDT)
Re: [AMBER] MCPB.py AmberTools17
(Sat Sep 23 2017 - 15:28:56 PDT)
Re: [AMBER] Question about MCPB.py
(Sat Sep 23 2017 - 15:14:04 PDT)
Re: [AMBER] SHAKE failure
(Sat Sep 23 2017 - 14:34:31 PDT)
Re: [AMBER] Antechamber RESP calculation error
(Sat Sep 23 2017 - 14:24:35 PDT)
Re: [AMBER] Mcpb.py for bay60 compound
(Tue Sep 19 2017 - 20:08:41 PDT)
Re: [AMBER] simulation time
(Tue Sep 19 2017 - 19:25:23 PDT)
Re: [AMBER] simulation time
(Tue Sep 19 2017 - 19:25:05 PDT)
Re: [AMBER] improper torsion terms
(Tue Sep 19 2017 - 19:20:45 PDT)
Re: [AMBER] TIP3p lennard jones parameters
(Mon Sep 11 2017 - 09:28:01 PDT)
Re: [AMBER] Moldeling with MCPB.py
(Tue Sep 05 2017 - 05:33:26 PDT)
R zu
[AMBER] Multiple Simulations on One GPU
(Fri Sep 29 2017 - 14:58:43 PDT)
Re: [AMBER] trajout last x frames cpptraj
(Thu Sep 28 2017 - 18:52:15 PDT)
Re: [AMBER] trajout last x frames cpptraj
(Thu Sep 28 2017 - 18:45:58 PDT)
[AMBER] barostat with large coupling constant
(Thu Sep 28 2017 - 18:14:57 PDT)
Re: [AMBER] Avoid pH Titration of LYS and TYR
(Thu Sep 28 2017 - 11:26:45 PDT)
Re: [AMBER] leaprc.constph and ff14sb
(Thu Sep 28 2017 - 11:16:48 PDT)
[AMBER] leaprc.constph and ff14sb
(Thu Sep 28 2017 - 08:06:18 PDT)
[AMBER] Avoid pH Titration of LYS and TYR
(Wed Sep 27 2017 - 12:17:21 PDT)
Rajarshi Roy
Re: [AMBER] Creation of unusual bonding via pdb4amber.
(Tue Sep 12 2017 - 22:52:43 PDT)
Re: [AMBER] Creation of unusual bonding via pdb4amber.
(Tue Sep 12 2017 - 20:56:29 PDT)
[AMBER] Creation of unusual bonding via pdb4amber.
(Tue Sep 12 2017 - 11:18:18 PDT)
Re: [AMBER] Residue wise energy decomposition via MM-PBSA
(Wed Sep 06 2017 - 00:20:34 PDT)
[AMBER] Residue wise energy decomposition via MM-PBSA
(Mon Sep 04 2017 - 21:06:49 PDT)
Rana Rehan Khalid
Re: [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command)
(Sat Sep 23 2017 - 14:39:07 PDT)
Re: [AMBER] Antechamber RESP calculation error
(Sat Sep 23 2017 - 14:36:21 PDT)
[AMBER] Antechamber RESP calculation error
(Sat Sep 23 2017 - 10:05:26 PDT)
Re: [AMBER] .com file creation
(Fri Sep 22 2017 - 14:34:32 PDT)
Re: [AMBER] mdcrd file not open in vmd
(Fri Sep 22 2017 - 11:23:13 PDT)
[AMBER] mdcrd file not open in vmd
(Fri Sep 22 2017 - 10:47:51 PDT)
Re: [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command)
(Fri Sep 22 2017 - 09:30:42 PDT)
[AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command)
(Fri Sep 22 2017 - 08:04:55 PDT)
Re: [AMBER] Antechamber
(Thu Sep 21 2017 - 13:57:20 PDT)
Re: [AMBER] Reduce command warnings Skipped hydrogen
(Thu Sep 21 2017 - 11:21:42 PDT)
[AMBER] Reduce command warnings Skipped hydrogen
(Thu Sep 21 2017 - 10:55:00 PDT)
Re: [AMBER] simulation stop due to size limit exceed
(Thu Sep 21 2017 - 09:17:54 PDT)
Re: [AMBER] Antechamber error
(Thu Sep 21 2017 - 09:03:28 PDT)
[AMBER] Antechamber error
(Thu Sep 21 2017 - 07:34:08 PDT)
[AMBER] simulation stop due to size limit exceed
(Thu Sep 21 2017 - 05:36:43 PDT)
Re: [AMBER] simulation of docked domains of protein
(Wed Sep 20 2017 - 12:45:17 PDT)
Re: [AMBER] Antechamber
(Wed Sep 20 2017 - 11:22:23 PDT)
Re: [AMBER] Antechamber
(Wed Sep 20 2017 - 11:02:02 PDT)
Re: [AMBER] Antechamber
(Wed Sep 20 2017 - 09:57:09 PDT)
[AMBER] Antechamber
(Wed Sep 20 2017 - 09:46:19 PDT)
[AMBER] simulation of docked domains of protein
(Wed Sep 20 2017 - 09:26:30 PDT)
[AMBER] .com file creation
(Tue Sep 19 2017 - 13:21:41 PDT)
[AMBER] Restart Simulation
(Tue Sep 19 2017 - 11:29:44 PDT)
Re: [AMBER] converting crd to pdb
(Tue Sep 19 2017 - 10:12:12 PDT)
[AMBER] converting crd to pdb
(Tue Sep 19 2017 - 10:05:21 PDT)
[AMBER] reduce command warnings
(Tue Sep 19 2017 - 08:13:30 PDT)
Re: [AMBER] Manually set residues Protonation states for HIS and CYS
(Mon Sep 18 2017 - 09:46:15 PDT)
Re: [AMBER] Manually set residues Protonation states for HIS and CYS
(Sun Sep 17 2017 - 12:30:16 PDT)
[AMBER] Manually set residues Protonation states for HIS and CYS
(Sun Sep 17 2017 - 12:27:46 PDT)
Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion)
(Sat Sep 16 2017 - 23:58:25 PDT)
Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion)
(Sat Sep 16 2017 - 12:30:28 PDT)
Re: [AMBER] Mcpb.py for bay60 compound
(Sat Sep 16 2017 - 12:20:08 PDT)
[AMBER] MCPB.py hbay.in input (system does not have metal ion)
(Sat Sep 16 2017 - 12:19:05 PDT)
Re: [AMBER] simulation time
(Sat Sep 16 2017 - 12:07:45 PDT)
Re: [AMBER] simulation time
(Sat Sep 16 2017 - 11:31:29 PDT)
[AMBER] Mcpb.py for bay60 compound
(Sat Sep 16 2017 - 10:43:17 PDT)
[AMBER] simulation time
(Sat Sep 16 2017 - 09:52:51 PDT)
Ravi Abrol
Re: [AMBER] How to save reimaged trajectory file during MD?
(Wed Sep 27 2017 - 11:35:41 PDT)
Re: [AMBER] How to save reimaged trajectory file during MD?
(Tue Sep 26 2017 - 06:37:27 PDT)
[AMBER] How to save reimaged trajectory file during MD?
(Mon Sep 25 2017 - 22:51:57 PDT)
Robin Betz
Re: [AMBER] Antechamber
(Wed Sep 20 2017 - 11:14:07 PDT)
Re: [AMBER] Can we specify the length and width of the water box in LEaP ?
(Mon Sep 11 2017 - 16:35:54 PDT)
Ross Walker
Re: [AMBER] Multiple Simulations on One GPU
(Sat Sep 30 2017 - 05:43:28 PDT)
Re: [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs
(Sat Sep 16 2017 - 07:00:21 PDT)
Re: [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs
(Tue Sep 12 2017 - 09:43:34 PDT)
Re: [AMBER] gamd.log for multiple runs
(Tue Sep 12 2017 - 09:15:18 PDT)
Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber
(Tue Sep 12 2017 - 06:43:50 PDT)
Re: [AMBER] NEW machine need help with GPU choice.
(Tue Sep 12 2017 - 06:09:01 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 10:05:21 PDT)
Saikat Pal
[AMBER] Is geometric center of atoms same as center of mass ?
(Sat Sep 16 2017 - 00:28:39 PDT)
[AMBER] significance of iwrap
(Fri Sep 01 2017 - 04:59:28 PDT)
Sanaa ALAbbad
Re: [AMBER] How tleap read a Ruthenium complex solvent box generated by packmol?
(Tue Sep 19 2017 - 15:32:31 PDT)
[AMBER] How tleap read a Ruthenium complex solvent box generated by packmol?
(Mon Sep 18 2017 - 15:18:03 PDT)
Sayuri Pacheco
Re: [AMBER] Cpptraj
(Thu Sep 28 2017 - 09:12:19 PDT)
[AMBER] Cpptraj
(Thu Sep 28 2017 - 09:01:42 PDT)
Scott Brozell
Re: [AMBER] Dr. Nick Riviera
(Wed Sep 27 2017 - 18:18:20 PDT)
Re: [AMBER] Antechamber error
(Thu Sep 21 2017 - 08:59:19 PDT)
Sebastian Franco Ulloa
Re: [AMBER] MMPBSA.py failing with topologies
(Thu Sep 14 2017 - 00:17:44 PDT)
Re: [AMBER] MMPBSA.py failing with topologies
(Wed Sep 13 2017 - 23:42:48 PDT)
[AMBER] MMPBSA error
(Mon Sep 11 2017 - 02:10:18 PDT)
[AMBER] MMPBSA.py failing with topologies
(Mon Sep 11 2017 - 01:46:18 PDT)
Sergey Samsonov
Re: [AMBER] Problem with MM-GBSA decomposition
(Thu Sep 28 2017 - 00:05:20 PDT)
[AMBER] Problem with MM-GBSA decomposition
(Tue Sep 26 2017 - 00:13:59 PDT)
Shafaq Muzammal
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 08:09:24 PDT)
Re: [AMBER] Minimization error due to modified residue
(Mon Sep 11 2017 - 07:57:48 PDT)
SHAILESH KUMAR
[AMBER] A query about coordinate saving frequency for solvation entropy calculation using GIST
(Tue Sep 26 2017 - 00:37:13 PDT)
Sharon D. Morris
[AMBER] Zinc dummy atom error in MMPBSA calculation
(Tue Sep 05 2017 - 22:26:13 PDT)
Shilpa Gupta
[AMBER] Frcmod file for ionic liquids
(Fri Sep 08 2017 - 21:43:05 PDT)
Sonata Kvedaravičiūtė
[AMBER] Pressure tensor
(Fri Sep 01 2017 - 01:43:48 PDT)
Sowmya Indrakumar
Re: [AMBER] cluster analysis using cpptraj
(Mon Sep 25 2017 - 07:00:20 PDT)
Re: [AMBER] cluster analysis using cpptraj
(Mon Sep 25 2017 - 02:55:57 PDT)
Re: [AMBER] cluster analysis using cpptraj
(Mon Sep 25 2017 - 02:47:51 PDT)
Re: [AMBER] cluster analysis using cpptraj
(Mon Sep 25 2017 - 02:38:52 PDT)
[AMBER] cluster analysis using cpptraj
(Mon Sep 25 2017 - 02:22:33 PDT)
[AMBER] angle between two subdomains
(Tue Sep 19 2017 - 06:44:11 PDT)
Steven M. Graham
[AMBER] PyRed
(Mon Sep 25 2017 - 18:42:18 PDT)
Tarsis
[AMBER] Using FEW with a transmembrane protein
(Mon Sep 25 2017 - 10:34:32 PDT)
Thakur, Abhishek
[AMBER] identifying the step of hbond interaction from trajectories
(Fri Sep 29 2017 - 11:20:24 PDT)
[AMBER] identiy the step of interaction from an entire trajectory
(Thu Sep 28 2017 - 12:10:47 PDT)
[AMBER] analysizing the trajectory for water interaction
(Mon Sep 25 2017 - 15:31:00 PDT)
[AMBER] water bridge analysis
(Mon Sep 25 2017 - 15:17:00 PDT)
[AMBER] .crd file format error
(Tue Sep 05 2017 - 08:37:15 PDT)
Thomas Cheatham
Re: [AMBER] cluster analysis using cpptraj
(Mon Sep 25 2017 - 02:47:51 PDT)
Timothy Schutt
Re: [AMBER] Is it possible to compile without linking C++ and fortran?
(Thu Sep 21 2017 - 15:12:04 PDT)
Re: [AMBER] [david.case.rutgers.edu: Re: Is it possible to compile without linking C++ and fortran?]
(Thu Sep 21 2017 - 14:15:31 PDT)
[AMBER] Is it possible to compile without linking C++ and fortran?
(Thu Sep 21 2017 - 10:56:19 PDT)
Re: [AMBER] Installing Compiling Errors
(Fri Sep 15 2017 - 09:56:08 PDT)
Re: [AMBER] Installing Compiling Errors
(Thu Sep 14 2017 - 15:00:25 PDT)
[AMBER] Installing Compiling Errors
(Thu Sep 14 2017 - 13:30:10 PDT)
waleed zalloum
[AMBER] moveanchor
(Thu Sep 28 2017 - 04:41:55 PDT)
Xing
Re: [AMBER] Can we specify the length and width of the water box in LEaP ?
(Mon Sep 11 2017 - 16:53:29 PDT)
[AMBER] Can we specify the length and width of the water box in LEaP ?
(Mon Sep 11 2017 - 16:27:45 PDT)
Yinglong Miao
Re: [AMBER] gamd.log for multiple runs
(Tue Sep 12 2017 - 11:28:40 PDT)
Zachary Smithline
[AMBER] Obtaining AM1-BCC charges in Antechamber
(Sat Sep 09 2017 - 23:33:14 PDT)
康宁
Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself
(Sun Sep 17 2017 - 18:47:37 PDT)
Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself
(Fri Sep 08 2017 - 18:04:24 PDT)
[AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself
(Thu Sep 07 2017 - 00:47:07 PDT)
杨满意
Re: [AMBER] How to calculate RDF with 'radial'
(Mon Sep 25 2017 - 04:44:12 PDT)
Re: [AMBER] How to calculate RDF with 'radial'
(Wed Sep 13 2017 - 18:49:49 PDT)
[AMBER] How to calculate RDF with 'radial'
(Tue Sep 12 2017 - 20:58:06 PDT)
鲁俊波
[AMBER] How to specify the liquid-liquid interface
(Mon Sep 18 2017 - 01:45:49 PDT)
Last message date
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Sat Sep 30 2017 - 06:00:03 PDT
Archived on
: Fri Nov 22 2024 - 05:55:31 PST
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