Amber Archive May 2018: by author

Aashish Bhatt
- [AMBER] Dimension Box visualization (Wed May 30 2018 - 23:00:50 PDT)
- Re: [AMBER] Error in using pdb4amber command (Thu May 24 2018 - 06:04:45 PDT)
- Re: [AMBER] Reg. generating empty frcmod file for ligand molecule (Thu May 17 2018 - 05:16:09 PDT)
ABEL Stephane
- Re: [AMBER] adding NME and ACE terminals (Wed May 09 2018 - 10:45:59 PDT)
- Re: [AMBER] adding NME and ACE terminals (Wed May 09 2018 - 10:36:28 PDT)
- Re: [AMBER] Poly amino acid helix form topology files (Mon May 07 2018 - 04:00:58 PDT)
- Re: [AMBER] Poly amino acid helix form topology files (Mon May 07 2018 - 03:02:53 PDT)
Abhilash J
- [AMBER] Initial configuration of ADP and ion simulation using AMBER. (Thu May 31 2018 - 09:45:12 PDT)
- Re: [AMBER] Simulation does not restart from restart file written in previous step. (Fri May 04 2018 - 05:19:38 PDT)
- Re: [AMBER] QM/MM minimization issue using sander (AMBER 18) (Tue May 01 2018 - 08:47:49 PDT)
- Re: [AMBER] QM/MM minimization issue using sander (AMBER 18) (Tue May 01 2018 - 06:03:28 PDT)
Alechania Misturini
- Re: [AMBER] Parametrization: consistency with gaff force field (Tue May 15 2018 - 04:55:07 PDT)
- [AMBER] Parametrization: consistency with gaff force field (Tue May 08 2018 - 11:25:50 PDT)
Alen Ahmetovic
- [AMBER] Troubleshooting SHAKE problems in minimization (Sat May 26 2018 - 21:07:29 PDT)
Ana Luisa Novo de Oliveira
- [AMBER] Scabilility of the code in cpus (Tue May 22 2018 - 09:45:39 PDT)
Andreas Tosstorff
- Re: [AMBER] nativecontacts command in CPPTRAJ (Wed May 23 2018 - 01:15:51 PDT)
- Re: [AMBER] nativecontacts command in CPPTRAJ (Sun May 06 2018 - 05:05:41 PDT)
andreas.tosstorff.cup.uni-muenchen.de
- [AMBER] Conda Installation error (Wed May 30 2018 - 10:51:25 PDT)
Antoine MARION
- Re: [AMBER] need QMMM interface for TURBOMOLE (Tue May 08 2018 - 08:19:17 PDT)
anu chandra
- [AMBER] Extracting infromation from topology file (Tue May 08 2018 - 22:36:23 PDT)
Aravind Ravichandran
- Re: [AMBER] TMD : Doubts regarding TGTMDFRC (Sun May 13 2018 - 23:44:25 PDT)
- [AMBER] TMD : Doubts regarding TGTMDFRC (Fri May 11 2018 - 23:25:58 PDT)
- [AMBER] Computing interaction energies from trajectory (Tue May 01 2018 - 06:59:32 PDT)
Bodee Nutho
- Re: [AMBER] QM/MM issue with boron containing compound (AMBER16) (Thu May 10 2018 - 19:02:07 PDT)
- [AMBER] QM/MM issue with boron containing compound (AMBER16) (Thu May 10 2018 - 08:04:32 PDT)
Carlos Simmerling
- Re: [AMBER] Request of help on Leap PDB preparation error "atom does not have a type" (Wed May 30 2018 - 05:09:31 PDT)
- Re: [AMBER] Reservoir REMD using GPUs (Fri May 25 2018 - 10:07:02 PDT)
- Re: [AMBER] Plotting phi-psi plots with free energy scale (Thu May 24 2018 - 07:13:33 PDT)
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? (Thu May 24 2018 - 06:53:04 PDT)
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? (Thu May 24 2018 - 05:56:20 PDT)
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? (Thu May 24 2018 - 05:17:26 PDT)
- Re: [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). (Thu May 17 2018 - 04:27:37 PDT)
- Re: [AMBER] TMD : Doubts regarding TGTMDFRC (Mon May 14 2018 - 05:12:01 PDT)
- Re: [AMBER] TMD : Doubts regarding TGTMDFRC (Sat May 12 2018 - 10:58:54 PDT)
- Re: [AMBER] Poly amino acid helix form topology files (Mon May 07 2018 - 04:59:51 PDT)
- Re: [AMBER] Poly amino acid helix form topology files (Sun May 06 2018 - 06:20:18 PDT)
- Re: [AMBER] Poly amino acid helix form topology files (Sun May 06 2018 - 06:01:08 PDT)
Charles Lin
- Re: [AMBER] Automatic patching failed! (Tue May 29 2018 - 22:11:09 PDT)
- Re: [AMBER] Automatic patching failed! (Tue May 29 2018 - 21:24:18 PDT)
- Re: [AMBER] GUI for TI setup (Mon May 14 2018 - 12:53:58 PDT)
Charo del Genio
- Re: [AMBER] Possible memory leak with LMOD (Wed May 23 2018 - 10:31:11 PDT)
- [AMBER] Possible memory leak with LMOD (Tue May 22 2018 - 09:39:08 PDT)
Chetna Tyagi
- [AMBER] Plotting phi-psi plots with free energy scale (Thu May 24 2018 - 07:01:19 PDT)
- Re: [AMBER] combining trajectories with different parameter files (Mon May 14 2018 - 05:17:12 PDT)
- [AMBER] combining trajectories with different parameter files (Mon May 14 2018 - 04:31:36 PDT)
- Re: [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem (Thu May 03 2018 - 07:36:12 PDT)
- [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem (Thu May 03 2018 - 07:18:54 PDT)
Chitrak Gupta
- [AMBER] lipid 14 MSD with OPC water (Sun May 13 2018 - 12:30:48 PDT)
- [AMBER] lipid MSD values for lipid 14 FF (Sat May 12 2018 - 14:56:12 PDT)
Chris Neale
- Re: [AMBER] Amber16 pmemd.cuda.MPI simulation can drop a frame with an inopportune node crash (Sat May 19 2018 - 15:04:04 PDT)
- [AMBER] Amber16 pmemd.cuda.MPI simulation can drop a frame with an inopportune node crash (Sat May 19 2018 - 00:07:06 PDT)
- Re: [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory (Thu May 10 2018 - 12:16:16 PDT)
- Re: [AMBER] what are the benefits of cuda9 vs. 8 with amber 18? (Wed May 09 2018 - 08:32:08 PDT)
- [AMBER] what are the benefits of cuda9 vs. 8 with amber 18? (Tue May 08 2018 - 21:41:11 PDT)
- [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory (Tue May 08 2018 - 16:58:41 PDT)
Cristián Ferretti
- [AMBER] problems with MCPY.py step 2 (Wed May 30 2018 - 03:03:02 PDT)
Cruzeiro,Vinicius Wilian D
- Re: [AMBER] AMBER: trouble while running constant pH simulation > (Cruzeiro, Vinicius Wilian D) (Wed May 30 2018 - 09:03:55 PDT)
- Re: [AMBER] AMBER: trouble while running constant pH simulation (Tue May 29 2018 - 05:58:06 PDT)
- Re: [AMBER] pmemd.MPI compatible for REMD simulation IN AMBER package (Wed May 16 2018 - 05:39:37 PDT)
Daniel Roe
- Re: [AMBER] nativecontacts command in CPPTRAJ (Tue May 22 2018 - 06:33:38 PDT)
- Re: [AMBER] Electrostatic potential calculation (Fri May 18 2018 - 07:49:11 PDT)
- Re: [AMBER] [cpptraj] Angle between atom and two centroids (Fri May 18 2018 - 05:05:26 PDT)
- Re: [AMBER] GPU questions (Thu May 17 2018 - 08:25:32 PDT)
- Re: [AMBER] autoimage problem (Wed May 16 2018 - 06:46:09 PDT)
- Re: [AMBER] combining trajectories with different parameter files (Mon May 14 2018 - 06:18:23 PDT)
- Re: [AMBER] Angle calculation between three amino acids (Fri May 11 2018 - 06:10:00 PDT)
- Re: [AMBER] MMPBSA.py execution error (Thu May 10 2018 - 11:15:38 PDT)
- Re: [AMBER] Error: No data sets selected - Problem or not? (Wed May 09 2018 - 05:25:27 PDT)
- Re: [AMBER] How to extract frames with particular hydrogen bonds only (Thu May 03 2018 - 07:42:05 PDT)
- Re: [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem (Thu May 03 2018 - 07:32:30 PDT)
- Re: [AMBER] CPPTRAJ Ensemble Keyword: "Too Many Open Files" (Thu May 03 2018 - 07:28:19 PDT)
daniele selli
- Re: [AMBER] Total Energy Decomposition (Wed May 23 2018 - 05:06:43 PDT)
- [AMBER] Total Energy Decomposition (Mon May 21 2018 - 04:06:56 PDT)
David A Case
- Re: [AMBER] Possible memory leak with LMOD (Thu May 31 2018 - 12:43:12 PDT)
- Re: [AMBER] Ubuntu 18 (Thu May 31 2018 - 07:10:58 PDT)
- Re: [AMBER] Dimension Box visualization (Thu May 31 2018 - 04:29:35 PDT)
- Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) (Thu May 31 2018 - 04:21:47 PDT)
- Re: [AMBER] Request of help on Leap PDB preparation error "atom does not have a type" (Wed May 30 2018 - 05:46:50 PDT)
- Re: [AMBER] Automatic patching failed! (Wed May 30 2018 - 05:42:42 PDT)
- Re: [AMBER] AMBER TI more examples (Tue May 29 2018 - 06:24:41 PDT)
- Re: [AMBER] Troubleshooting SHAKE problems in minimization (Sun May 27 2018 - 06:06:47 PDT)
- Re: [AMBER] Using multiple CPU threads (Sat May 26 2018 - 06:19:21 PDT)
- Re: [AMBER] CUDA v9.0 with AMBER16 Question (Sat May 26 2018 - 06:14:01 PDT)
- Re: [AMBER] Error in using pdb4amber command (Thu May 24 2018 - 04:49:10 PDT)
- Re: [AMBER] optimization of QM zone in QM/MM-GBSA calculations. (Thu May 24 2018 - 04:46:03 PDT)
- Re: [AMBER] update_amber URL time out problem (Thu May 24 2018 - 04:45:05 PDT)
- Re: [AMBER] pmemd.MPI won't work in Amber 18 (Thu May 24 2018 - 04:38:09 PDT)
- Re: [AMBER] Amber 18 manual shows TI as not supported in pmemd.cuda (Thu May 24 2018 - 04:34:27 PDT)
- Re: [AMBER] Possible memory leak with LMOD (Thu May 24 2018 - 04:31:06 PDT)
- Re: [AMBER] Use of Amber12 and 14 on the same simulation (Thu May 24 2018 - 04:28:45 PDT)
- Re: [AMBER] update_amber URL time out problem (Wed May 23 2018 - 05:13:09 PDT)
- Re: [AMBER] Hydrogen Bond Occupancy (Tue May 22 2018 - 17:46:00 PDT)
- Re: [AMBER] Creating a Gold surface library file (Tue May 22 2018 - 17:43:01 PDT)
- Re: [AMBER] R: Re: SHAKEH: Extra bond between hydrogen atoms of TIP3 water model (Tue May 22 2018 - 17:32:17 PDT)
- Re: [AMBER] Scabilility of the code in cpus (Tue May 22 2018 - 13:38:59 PDT)
- Re: [AMBER] Possible memory leak with LMOD (Tue May 22 2018 - 13:08:59 PDT)
- Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model (Tue May 22 2018 - 12:53:54 PDT)
- Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda (Tue May 22 2018 - 12:21:31 PDT)
- Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model (Tue May 22 2018 - 05:15:20 PDT)
- Re: [AMBER] Total Energy Decomposition (Tue May 22 2018 - 05:12:46 PDT)
- Re: [AMBER] Creating a Gold surface library file (Sat May 19 2018 - 06:53:59 PDT)
- Re: [AMBER] Facing problem to generate ala10_chir.dat in REMD tutorial (Fri May 18 2018 - 07:03:50 PDT)
- Re: [AMBER] NetCDF error: NetCDF: Not a valid ID (Fri May 18 2018 - 05:34:43 PDT)
- Re: [AMBER] I: help please (Fri May 18 2018 - 05:18:16 PDT)
- Re: [AMBER] DFT method for calculating amino acids partial charges in AMBER99 (Fri May 18 2018 - 05:10:07 PDT)
- Re: [AMBER] [cpptraj] Angle between atom and two centroids (Fri May 18 2018 - 05:04:34 PDT)
- Re: [AMBER] Parametrization of Small Molecules (Fri May 18 2018 - 04:58:13 PDT)
- Re: [AMBER] Creating a Gold surface library file (Fri May 18 2018 - 04:51:42 PDT)
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" (Thu May 17 2018 - 09:11:23 PDT)
- Re: [AMBER] MD stops due to the distortion of a molecule (Thu May 17 2018 - 05:11:48 PDT)
- Re: [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). (Thu May 17 2018 - 05:02:00 PDT)
- Re: [AMBER] autoimage problem (Wed May 16 2018 - 05:59:17 PDT)
- Re: [AMBER] MMPBSA.py - PrmtopError: Inconsistent charge definition for atom (Wed May 16 2018 - 05:49:18 PDT)
- Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda (Tue May 15 2018 - 13:12:53 PDT)
- Re: [AMBER] Creating a Gold surface library file (Mon May 14 2018 - 18:20:45 PDT)
- Re: [AMBER] Parametrization: consistency with gaff force field (Mon May 14 2018 - 07:25:43 PDT)
- Re: [AMBER] combining trajectories with different parameter files (Mon May 14 2018 - 05:09:20 PDT)
- Re: [AMBER] tleap error 'FATAL: Atom .R<NMET 1>.A<CAY 20> does not have a type' (Mon May 14 2018 - 05:06:22 PDT)
- Re: [AMBER] Novice Question: MD Visualisation in VMD (Sun May 13 2018 - 10:59:33 PDT)
- Re: [AMBER] change the charge of the chlorine ion (Sat May 12 2018 - 10:13:23 PDT)
- Re: [AMBER] MMPBSA.py execution error (Thu May 10 2018 - 12:11:56 PDT)
- Re: [AMBER] QM/MM issue with boron containing compound (AMBER16) (Thu May 10 2018 - 11:48:01 PDT)
- Re: [AMBER] Different outputs of external electric field (Thu May 10 2018 - 06:05:56 PDT)
- Re: [AMBER] Different outputs of external electric field (Thu May 10 2018 - 04:17:56 PDT)
- Re: [AMBER] Multiple temperature groups (Wed May 09 2018 - 18:52:59 PDT)
- Re: [AMBER] Amber 18 Thermodynamic integration question (Wed May 09 2018 - 07:29:18 PDT)
- Re: [AMBER] adding NME and ACE terminals (Wed May 09 2018 - 07:23:48 PDT)
- Re: [AMBER] Different outputs of external electric field (Wed May 09 2018 - 07:20:33 PDT)
- Re: [AMBER] what are the benefits of cuda9 vs. 8 with amber 18? (Wed May 09 2018 - 07:18:28 PDT)
- Re: [AMBER] Setting initial velocities (Wed May 09 2018 - 05:27:58 PDT)
- Re: [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory (Wed May 09 2018 - 05:20:48 PDT)
- Re: [AMBER] need QMMM interface for TURBOMOLE (Mon May 07 2018 - 04:39:11 PDT)
- Re: [AMBER] SGLD (Sat May 05 2018 - 19:10:14 PDT)
- Re: [AMBER] Problem in distance restraint (Fri May 04 2018 - 10:47:07 PDT)
- Re: [AMBER] AMBER Digest, Vol 2280, Issue 1 (Fri May 04 2018 - 05:21:02 PDT)
- Re: [AMBER] Configure CUDA issues (Thu May 03 2018 - 10:35:32 PDT)
- Re: [AMBER] .rst and .mdcrd file outputted in ascii (Wed May 02 2018 - 11:36:59 PDT)
- Re: [AMBER] update ambertools (Wed May 02 2018 - 05:26:34 PDT)
- Re: [AMBER] GPU benchmark - Amber18 (Wed May 02 2018 - 05:18:39 PDT)
- Re: [AMBER] Boost not linking when compiling on Mac (Wed May 02 2018 - 04:48:41 PDT)
David Adrian Saez San Martin
- Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda (Mon May 14 2018 - 18:58:02 PDT)
David Cerutti
- Re: [AMBER] Amber16 pmemd.cuda.MPI simulation can drop a frame with an inopportune node crash (Sat May 19 2018 - 04:30:27 PDT)
David Sáez
- [AMBER] parmed/chamber verify including CMAP corrections (Wed May 23 2018 - 12:00:26 PDT)
- [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda (Mon May 14 2018 - 18:49:05 PDT)
David Wifling
- [AMBER] Amber 18 Thermodynamic integration question (Mon May 07 2018 - 12:27:18 PDT)
DHEERAJ CHITARA
- Re: [AMBER] Reg. generating empty frcmod file for ligand molecule (Thu May 17 2018 - 05:40:57 PDT)
- Re: [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). (Thu May 17 2018 - 05:08:50 PDT)
- [AMBER] Reg. generating empty frcmod file for ligand molecule (Thu May 17 2018 - 05:03:01 PDT)
- Re: [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). (Thu May 17 2018 - 04:41:08 PDT)
- [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). (Thu May 17 2018 - 01:04:54 PDT)
diego.soler.uam.es
- [AMBER] Setting initial velocities (Fri May 04 2018 - 05:42:39 PDT)
Eiros Zamora, Juan
- [AMBER] [cpptraj] Angle between atom and two centroids (Fri May 18 2018 - 04:14:11 PDT)
Feng Pan
- Re: [AMBER] AMBER NFE SMD calculation with new collective variable (Wed May 30 2018 - 11:20:39 PDT)
- Re: [AMBER] ABMD with multiple walkers (Mon May 28 2018 - 18:01:21 PDT)
- Re: [AMBER] ABMD with multiple walkers (Sun May 27 2018 - 19:05:45 PDT)
- Re: [AMBER] ABMD with multiple walkers (Sat May 26 2018 - 19:16:09 PDT)
- Re: [AMBER] Using infe = 1, &pmd, and pmemd.cuda (AMBER16) (Wed May 02 2018 - 13:40:13 PDT)
FyD
- Re: [AMBER] S-S bond (Wed May 23 2018 - 22:24:55 PDT)
- Re: [AMBER] DFT method for calculating amino acids partial charges in AMBER99 (Thu May 17 2018 - 03:19:32 PDT)
georg.kuenze.vanderbilt.edu
- [AMBER] AMBER NFE SMD calculation with new collective variable (Mon May 28 2018 - 13:51:41 PDT)
giuseppe gatti
- [AMBER] I: help please (Wed May 16 2018 - 08:10:19 PDT)
Goetz, Andreas
- Re: [AMBER] need QMMM interface for TURBOMOLE (Mon May 07 2018 - 10:26:15 PDT)
- Re: [AMBER] QM/MM minimization issue using sander (AMBER 18) (Mon Apr 30 2018 - 17:01:55 PDT)
Gustaf Olsson
- Re: [AMBER] Request of help on Leap PDB preparation error "atom does not have a type" (Tue May 29 2018 - 23:36:40 PDT)
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? (Thu May 24 2018 - 05:19:18 PDT)
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? (Thu May 24 2018 - 05:15:47 PDT)
- Re: [AMBER] VMD window (Wed May 23 2018 - 00:48:40 PDT)
- Re: [AMBER] Hydrogen Bond Occupancy (Tue May 22 2018 - 23:27:45 PDT)
- Re: [AMBER] VMD window (Tue May 22 2018 - 23:05:11 PDT)
- Re: [AMBER] Error: No data sets selected - Problem or not? (Wed May 09 2018 - 05:34:07 PDT)
- [AMBER] Error: No data sets selected - Problem or not? (Wed May 09 2018 - 04:15:55 PDT)
- Re: [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem (Thu May 03 2018 - 07:28:47 PDT)
- Re: [AMBER] Boost not linking when compiling on Mac (Wed May 02 2018 - 05:53:36 PDT)
- Re: [AMBER] Boost not linking when compiling on Mac (Tue May 01 2018 - 23:44:30 PDT)
Hadházi Ádám
- Re: [AMBER] 1x PCI-E Riser card for MD/TI? (Tue May 22 2018 - 14:42:29 PDT)
- [AMBER] 1x PCI-E Riser card for MD/TI? (Tue May 22 2018 - 07:20:46 PDT)
- [AMBER] GUI for TI setup (Mon May 14 2018 - 06:38:43 PDT)
- [AMBER] GPU benchmark - Amber18 (Wed May 02 2018 - 02:00:19 PDT)
Hai Long
- Re: [AMBER] pmemd.MPI won't work in Amber 18 (Thu May 24 2018 - 14:44:40 PDT)
- [AMBER] pmemd.MPI won't work in Amber 18 (Wed May 23 2018 - 14:37:27 PDT)
Hai Nguyen
- Re: [AMBER] Conda Installation error (Thu May 31 2018 - 09:11:38 PDT)
- Re: [AMBER] Conda Installation error (Thu May 31 2018 - 07:18:30 PDT)
- Re: [AMBER] MMPBSA.py execution error (Thu May 10 2018 - 13:24:22 PDT)
- Re: [AMBER] Extracting infromation from topology file (Tue May 08 2018 - 22:47:07 PDT)
- Re: [AMBER] Setting initial velocities (Tue May 08 2018 - 20:22:29 PDT)
- Re: [AMBER] Setting initial velocities (Tue May 08 2018 - 20:18:27 PDT)
Holger Kruse
- Re: [AMBER] need QMMM interface for TURBOMOLE (Wed May 09 2018 - 05:26:25 PDT)
Horn, Anselm
- Re: [AMBER] Novice Question: MD Visualisation in VMD (Sun May 13 2018 - 05:07:40 PDT)
Hurst, Travis C (MU-Student)
- Re: [AMBER] Reservoir REMD using GPUs (Tue May 29 2018 - 08:09:01 PDT)
- [AMBER] Reservoir REMD using GPUs (Wed May 16 2018 - 15:25:55 PDT)
I Lőrincz
- [AMBER] Multiple temperature groups (Thu May 03 2018 - 07:03:13 PDT)
James Kress
- Re: [AMBER] GUI for TI setup (Mon May 14 2018 - 14:11:00 PDT)
- Re: [AMBER] Novice Question: MD Visualisation in VMD (Sun May 13 2018 - 12:18:14 PDT)
Jason Ku Wang
- [AMBER] CPPTRAJ Ensemble Keyword: "Too Many Open Files" (Tue May 01 2018 - 16:55:15 PDT)
Jerrano Bowleg
- Re: [AMBER] Hydrogen Bond Occupancy (Wed May 23 2018 - 06:44:22 PDT)
- [AMBER] Hydrogen Bond Occupancy (Tue May 22 2018 - 10:13:42 PDT)
Jiri Sponer
- [AMBER] PhD/Junior position, AMBER sims DNA/RNA (Wed May 02 2018 - 03:54:35 PDT)
Jissy Akkarapattiakal Kuriappan
- [AMBER] TiMergeError: Cannot have dihedral cross through softcore region (Wed May 30 2018 - 06:07:15 PDT)
JoAnne Babula
- [AMBER] Use of Amber12 and 14 on the same simulation (Wed May 23 2018 - 09:09:08 PDT)
Johannes Loeffler
- [AMBER] Parametrization of Small Molecules (Fri May 18 2018 - 02:44:56 PDT)
Jose Manuel Granadino Roldán
- Re: [AMBER] MMPBSA.py execution error (Fri May 11 2018 - 00:27:52 PDT)
- [AMBER] MMPBSA.py execution error (Thu May 10 2018 - 09:14:27 PDT)
- [AMBER] GBNSR6 with MMPBSA.py (Tue May 08 2018 - 02:08:38 PDT)
Josephine la sala
- [AMBER] TI for side chain mutation in dimer protein (Wed May 30 2018 - 06:29:22 PDT)
- [AMBER] TI for side chain mutation in dimer protein (Wed May 30 2018 - 02:55:48 PDT)
Juan Eiros
- Re: [AMBER] adding NME and ACE terminals (Wed May 09 2018 - 03:56:23 PDT)
Kadir Ozcan
- Re: [AMBER] AMBER Digest, Vol 2280, Issue 1 (Thu May 03 2018 - 15:19:23 PDT)
- Re: [AMBER] Configure CUDA issues (Thu May 03 2018 - 08:55:34 PDT)
Karla Galdamez
- Re: [AMBER] VMD window (Wed May 23 2018 - 07:24:27 PDT)
- Re: [AMBER] VMD window (Tue May 22 2018 - 23:53:14 PDT)
- [AMBER] VMD window (Tue May 22 2018 - 20:43:23 PDT)
- Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model (Mon May 21 2018 - 18:54:49 PDT)
Kasprzak, Wojciech (NIH/NCI) [C]
- [AMBER] MMPBSA.py.MPI: questions about output warnings and discrepancies (Fri May 11 2018 - 06:59:40 PDT)
- [AMBER] MMPBSA.py.MPI and matching topology files a problem (Tue May 08 2018 - 09:17:21 PDT)
Kenneth Huang
- [AMBER] PC modes per residue from existing evecs file? (Mon May 07 2018 - 08:15:27 PDT)
- Re: [AMBER] calculation of cavity water (Mon May 07 2018 - 07:47:36 PDT)
- Re: [AMBER] calculation of cavity water (Sun May 06 2018 - 07:35:01 PDT)
- Re: [AMBER] calculation of cavity water (Sun May 06 2018 - 07:28:37 PDT)
- Re: [AMBER] calculation of cavity water (Fri May 04 2018 - 13:15:16 PDT)
Kevin Keane
- Re: [AMBER] update ambertools (Wed May 02 2018 - 10:20:30 PDT)
Korey M Reid
- [AMBER] CUDA v9.0 with AMBER16 Question (Fri May 25 2018 - 16:56:43 PDT)
koushik kasavajhala
- Re: [AMBER] Reservoir REMD using GPUs (Thu May 31 2018 - 12:47:15 PDT)
Kshatresh Dutta Dubey
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? (Thu May 24 2018 - 06:27:03 PDT)
- [AMBER] Problem in distance restraint (Fri May 04 2018 - 05:01:57 PDT)
Leena Aggarwal
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" (Thu May 17 2018 - 21:36:09 PDT)
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" (Thu May 17 2018 - 06:23:15 PDT)
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" (Thu May 17 2018 - 05:06:37 PDT)
- Re: [AMBER] calculation of cavity water (Fri May 04 2018 - 21:13:08 PDT)
Lei Zhao
- [AMBER] How to evaluate the impact of PH on protein structures by Amber (Thu May 24 2018 - 07:49:38 PDT)
Lenz, Stefan
- [AMBER] Using infe = 1, &pmd, and pmemd.cuda (AMBER16) (Tue May 01 2018 - 09:04:27 PDT)
Markowska
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? (Fri May 25 2018 - 05:37:18 PDT)
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? (Thu May 24 2018 - 06:07:13 PDT)
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? (Thu May 24 2018 - 05:52:59 PDT)
- [AMBER] How to prepare prmtop and inpcrd files from a PDB file? (Thu May 24 2018 - 05:07:20 PDT)
maryam azimzadehirani
- Re: [AMBER] Angle calculation between three amino acids (Fri May 11 2018 - 06:35:05 PDT)
- [AMBER] Angle calculation between three amino acids (Thu May 10 2018 - 23:45:27 PDT)
Matias Machado
- Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) (Thu May 31 2018 - 05:10:54 PDT)
- Re: [AMBER] Dimension Box visualization (Thu May 31 2018 - 04:45:13 PDT)
- Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) (Wed May 30 2018 - 19:12:28 PDT)
Meng Wu
- Re: [AMBER] update_amber URL time out problem (Wed May 23 2018 - 20:07:55 PDT)
- [AMBER] update_amber URL time out problem (Wed May 23 2018 - 01:29:11 PDT)
- Re: [AMBER] Electrostatic potential calculation (Thu May 17 2018 - 23:45:54 PDT)
- [AMBER] Electrostatic potential calculation (Tue May 15 2018 - 19:52:18 PDT)
- Re: [AMBER] Different outputs of external electric field (Wed May 09 2018 - 20:16:44 PDT)
- [AMBER] Different outputs of external electric field (Wed May 09 2018 - 04:05:42 PDT)
Midhun K Madhu
- Re: [AMBER] Restart From Check point File (Mon May 21 2018 - 22:22:46 PDT)
- [AMBER] Restart From Check point File (Sun May 20 2018 - 05:47:24 PDT)
- [AMBER] NetCDF error: NetCDF: Not a valid ID (Mon May 14 2018 - 14:12:46 PDT)
- [AMBER] tleap error 'FATAL: Atom .R<NMET 1>.A<CAY 20> does not have a type' (Mon May 14 2018 - 00:26:01 PDT)
Ming Tang
- [AMBER] autoimage problem (Mon May 14 2018 - 06:59:14 PDT)
mish
- [AMBER] optimization of QM zone in QM/MM-GBSA calculations. (Thu May 24 2018 - 00:10:19 PDT)
Omoto, Kiyoyuki
- [AMBER] AMBER TI more examples (Thu May 24 2018 - 08:30:55 PDT)
Patricio German Barletta Roldan
- [AMBER] Amber 18 manual shows TI as not supported in pmemd.cuda (Wed May 23 2018 - 13:47:48 PDT)
Piotr Fajer
- Re: [AMBER] SGLD (Sat May 05 2018 - 19:19:12 PDT)
- [AMBER] SGLD (Sat May 05 2018 - 12:52:40 PDT)
PRITI ROY
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" (Thu May 17 2018 - 22:22:51 PDT)
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" (Thu May 17 2018 - 09:18:50 PDT)
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" (Thu May 17 2018 - 06:04:08 PDT)
- [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" (Thu May 17 2018 - 02:45:51 PDT)
Qinghua Liao
- Re: [AMBER] ABMD with multiple walkers (Tue May 29 2018 - 00:31:31 PDT)
- Re: [AMBER] ABMD with multiple walkers (Mon May 28 2018 - 05:36:21 PDT)
- Re: [AMBER] ABMD with multiple walkers (Sun May 27 2018 - 14:08:12 PDT)
- [AMBER] ABMD with multiple walkers (Fri May 25 2018 - 16:00:01 PDT)
Robin Betz
- Re: [AMBER] parmed/chamber verify including CMAP corrections (Wed May 23 2018 - 12:06:19 PDT)
Rodrigo Galindo-Murillo
- [AMBER] MMPBSA.py - PrmtopError: Inconsistent charge definition for atom (Tue May 15 2018 - 14:41:50 PDT)
roja rahmani
- Re: [AMBER] S-S bond (Wed May 23 2018 - 22:45:13 PDT)
- [AMBER] S-S bond (Wed May 23 2018 - 02:47:29 PDT)
- Re: [AMBER] DFT method for calculating amino acids partial charges in AMBER99 (Fri May 18 2018 - 05:33:26 PDT)
- [AMBER] DFT method for calculating amino acids partial charges in AMBER99 (Thu May 17 2018 - 03:10:43 PDT)
- Re: [AMBER] adding NME and ACE terminals (Wed May 09 2018 - 10:41:15 PDT)
- Re: [AMBER] adding NME and ACE terminals (Wed May 09 2018 - 08:53:15 PDT)
- Re: [AMBER] adding NME and ACE terminals (Wed May 09 2018 - 05:21:18 PDT)
- Re: [AMBER] adding NME and ACE terminals (Wed May 09 2018 - 05:08:59 PDT)
- [AMBER] adding NME and ACE terminals (Wed May 09 2018 - 03:40:10 PDT)
- Re: [AMBER] Poly amino acid helix form topology files (Mon May 07 2018 - 03:19:01 PDT)
- Re: [AMBER] Poly amino acid helix form topology files (Sun May 06 2018 - 06:29:52 PDT)
- Re: [AMBER] Poly amino acid helix form topology files (Sun May 06 2018 - 06:15:12 PDT)
- [AMBER] Poly amino acid helix form topology files (Sat May 05 2018 - 23:53:31 PDT)
Rosellen, Martin
- [AMBER] info grafic about MD (Mon May 21 2018 - 05:45:42 PDT)
Ross Walker
- Re: [AMBER] pmemd.MPI won't work in Amber 18 (Thu May 24 2018 - 15:08:11 PDT)
- Re: [AMBER] 1x PCI-E Riser card for MD/TI? (Tue May 22 2018 - 14:08:48 PDT)
Ruth Helena Tichauer
- Re: [AMBER] nativecontacts command in CPPTRAJ (Wed May 23 2018 - 08:28:49 PDT)
- Re: [AMBER] nativecontacts command in CPPTRAJ (Wed May 23 2018 - 01:43:43 PDT)
- Re: [AMBER] nativecontacts command in CPPTRAJ (Wed May 23 2018 - 01:09:47 PDT)
- Re: [AMBER] nativecontacts command in CPPTRAJ (Tue May 22 2018 - 06:25:33 PDT)
- Re: [AMBER] nativecontacts command in CPPTRAJ (Sun May 06 2018 - 08:58:09 PDT)
- Re: [AMBER] nativecontacts command in CPPTRAJ (Sun May 06 2018 - 07:57:01 PDT)
- [AMBER] nativecontacts command in CPPTRAJ (Sun May 06 2018 - 03:31:06 PDT)
Sadegh Faramarzi Ganjabad
- Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model (Mon May 28 2018 - 13:29:46 PDT)
- Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model (Wed May 23 2018 - 12:36:30 PDT)
- [AMBER] R: Re: SHAKEH: Extra bond between hydrogen atoms of TIP3 water model (Tue May 22 2018 - 12:59:21 PDT)
- [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model (Mon May 21 2018 - 11:24:52 PDT)
Saikat Pal
- [AMBER] Facing problem to generate ala10_chir.dat in REMD tutorial (Fri May 18 2018 - 05:29:21 PDT)
- [AMBER] pmemd.MPI compatible for REMD simulation IN AMBER package (Tue May 15 2018 - 22:48:07 PDT)
- Re: [AMBER] change the charge of the chlorine ion (Sun May 13 2018 - 21:43:43 PDT)
- [AMBER] change the charge of the chlorine ion (Sat May 12 2018 - 05:13:21 PDT)
- [AMBER] Query related to the Umbrella sampling method (Tue May 08 2018 - 23:00:50 PDT)
Scott Brozell
- Re: [AMBER] Conda Installation error (Thu May 31 2018 - 09:18:24 PDT)
- Re: [AMBER] Conda Installation error (Thu May 31 2018 - 09:06:54 PDT)
- Re: [AMBER] Ubuntu 18 (Thu May 31 2018 - 08:55:40 PDT)
- Re: [AMBER] need QMMM interface for TURBOMOLE (Tue May 08 2018 - 12:47:04 PDT)
- Re: [AMBER] Boost not linking when compiling on Mac (Wed May 02 2018 - 17:30:23 PDT)
senal dinuka
- Re: [AMBER] Automatic patching failed! (Wed May 30 2018 - 00:49:40 PDT)
- Re: [AMBER] Automatic patching failed! (Tue May 29 2018 - 21:30:50 PDT)
- [AMBER] Automatic patching failed! (Tue May 29 2018 - 21:10:54 PDT)
- [AMBER] Using multiple CPU threads (Sat May 26 2018 - 01:17:55 PDT)
- Re: [AMBER] Error in using pdb4amber command (Thu May 24 2018 - 04:55:14 PDT)
- [AMBER] Error in using pdb4amber command (Thu May 24 2018 - 03:14:03 PDT)
- [AMBER] Advice on SMD QM/MM for Cyanogenic Glucoside (Mon May 07 2018 - 23:34:21 PDT)
Sepideh Jafari
- Re: [AMBER] Ubuntu 18 (Thu May 31 2018 - 07:29:24 PDT)
- [AMBER] Ubuntu 18 (Thu May 31 2018 - 06:22:00 PDT)
Sergey Samsonov
- Re: [AMBER] MD stops due to the distortion of a molecule (Thu May 17 2018 - 23:13:43 PDT)
- [AMBER] MD stops due to the distortion of a molecule (Thu May 17 2018 - 01:23:57 PDT)
Sowmya Indrakumar
- Re: [AMBER] nativecontacts command in CPPTRAJ (Sun May 06 2018 - 09:26:52 PDT)
- Re: [AMBER] nativecontacts command in CPPTRAJ (Sun May 06 2018 - 08:13:32 PDT)
Stefan.Guessregen.sanofi.com
- [AMBER] DEADLINE EXTENDED: Call for Papers, GCC 2018, 14th German Conference on Chemoinformatics (Mon May 28 2018 - 04:56:58 PDT)
Stejskal, Lenka
- [AMBER] How to extract frames with particular hydrogen bonds only (Wed May 02 2018 - 08:31:59 PDT)
Stephan Schott
- Re: [AMBER] error in rst file during Minimization (Mon May 28 2018 - 06:03:57 PDT)
- Re: [AMBER] Restart From Check point File (Tue May 22 2018 - 05:36:12 PDT)
- Re: [AMBER] Restart From Check point File (Sun May 20 2018 - 08:27:10 PDT)
Subrata Paul
- Re: [AMBER] error in rst file during Minimization (Mon May 28 2018 - 09:04:38 PDT)
- [AMBER] error in rst file during Minimization (Mon May 28 2018 - 05:37:08 PDT)
Thomas Exner
- Re: [AMBER] eCheminfo Oxford, UK Training and Innovation Course in Drug Design 2018, first announcement (Wed May 30 2018 - 02:59:48 PDT)
- Re: [AMBER] eCheminfo Milano July 16-29, Training and Innovation Course in Drug Design 2018, bursary and early-bird deadline ending soon (Thu May 24 2018 - 04:43:18 PDT)
Timothy Cholko
- Re: [AMBER] Creating a Gold surface library file (Tue May 22 2018 - 15:37:29 PDT)
- Re: [AMBER] Creating a Gold surface library file (Fri May 18 2018 - 15:03:41 PDT)
- Re: [AMBER] Creating a Gold surface library file (Thu May 17 2018 - 14:49:53 PDT)
- [AMBER] Creating a Gold surface library file (Mon May 14 2018 - 17:35:06 PDT)
Tom Kurtzman
- Re: [AMBER] calculation of cavity water (Mon May 07 2018 - 09:13:15 PDT)
Tousif Hossen
- Re: [AMBER] calculation of cavity water (Mon May 07 2018 - 11:09:26 PDT)
- Re: [AMBER] calculation of cavity water (Mon May 07 2018 - 08:22:41 PDT)
- Re: [AMBER] calculation of cavity water (Mon May 07 2018 - 06:38:35 PDT)
- Re: [AMBER] calculation of cavity water (Sun May 06 2018 - 22:41:24 PDT)
- Re: [AMBER] calculation of cavity water (Sat May 05 2018 - 23:29:43 PDT)
- [AMBER] calculation of cavity water (Fri May 04 2018 - 04:11:33 PDT)
- [AMBER] update Ambertools (Wed May 02 2018 - 02:33:16 PDT)
- [AMBER] update ambertools (Wed May 02 2018 - 02:28:52 PDT)
Tyler Luchko (Lists)
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" (Thu May 17 2018 - 08:47:57 PDT)
Urszula Uciechowska
- [AMBER] sander failed with prmtop complex.top! (Tue May 29 2018 - 23:52:54 PDT)
Vivek Bharadwaj
- Re: [AMBER] Cremer Pucker values using Pytraj (Tue May 01 2018 - 07:31:34 PDT)
Yuxin Xie
- [AMBER] MMPBSA energy decomposition (Wed May 16 2018 - 11:38:47 PDT)
李耀
- Re: [AMBER] AMBER: trouble while running constant pH simulation > (Cruzeiro, Vinicius Wilian D) (Wed May 30 2018 - 08:48:29 PDT)
- Re: [AMBER] AMBER: trouble while running constant pH simulation (Tue May 29 2018 - 00:54:18 PDT)
- [AMBER] AMBER: trouble while running constant pH simulation (Mon May 28 2018 - 19:35:06 PDT)
符哲瀚
- [AMBER] Request of help on Leap PDB preparation error "atom does not have a type" (Tue May 29 2018 - 21:32:33 PDT)
陈金峰
- [AMBER] QMMM surface scan (Fri May 18 2018 - 07:55:39 PDT)
- [AMBER] GPU questions (Thu May 17 2018 - 07:54:17 PDT)
- [AMBER] need QMMM interface for TURBOMOLE (Wed May 02 2018 - 16:38:09 PDT)

Amber Archive May 2018 by author