Amber Archive Nov 2016: by author

Abdul Ajees
- [AMBER] Coordinates for PEG4K, Folic acid and chitin (Tue Nov 08 2016 - 03:02:37 PST)
Abhi Acharya
- Re: [AMBER] Query regarding the MCPB.py workflow (Sat Nov 19 2016 - 22:34:34 PST)
- Re: [AMBER] Query regarding the MCPB.py workflow (Wed Nov 16 2016 - 02:45:23 PST)
- [AMBER] Query regarding the MCPB.py workflow (Sat Nov 12 2016 - 01:09:19 PST)
ABHIJEET CHOWDHURY
- Re: [AMBER] Converting coordinate file generated into pdb format for nuparm (Thu Nov 17 2016 - 06:52:33 PST)
- Re: [AMBER] Converting coordinate file generated into pdb format for nuparm (Thu Nov 17 2016 - 06:39:02 PST)
- [AMBER] Converting coordinate file generated into pdb format for nuparm (Thu Nov 17 2016 - 04:43:59 PST)
Aditya G Rao
- Re: [AMBER] Can we combine amber and gaff atom types? (Thu Nov 03 2016 - 09:39:58 PDT)
- Re: [AMBER] Can we combine amber and gaff atom types? (Wed Nov 02 2016 - 06:55:12 PDT)
Adrian Roitberg
- Re: [AMBER] RMSD for two different MDs (Mon Nov 28 2016 - 13:32:23 PST)
- Re: [AMBER] more on the Berendsen thermostat (Wed Nov 23 2016 - 10:48:49 PST)
- Re: [AMBER] DIfferences between thermostats (Tue Nov 22 2016 - 15:28:14 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 10:38:58 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 09:59:54 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 09:54:34 PST)
- Re: [AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day (Tue Nov 15 2016 - 07:06:36 PST)
- Re: [AMBER] Filename being truncated by pmemd.cuda (Mon Nov 14 2016 - 08:16:25 PST)
- Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? (Mon Nov 07 2016 - 06:02:17 PST)
- Re: [AMBER] Failed to install mpirun (Thu Nov 03 2016 - 11:00:19 PDT)
Ahsan Mohd
- [AMBER] covalently bound ligand (Mon Nov 14 2016 - 10:20:14 PST)
Aishani Prem
- [AMBER] mdfil: Error unknown flag: pdb_wat.prmtop (Wed Nov 30 2016 - 15:32:29 PST)
amaury paquet
- [AMBER] question about calculated density in sander output file (Wed Nov 30 2016 - 06:22:01 PST)
Amy Rice
- Re: [AMBER] Convert prm into prmtop - from NAMD to AMBER (Mon Nov 21 2016 - 11:39:05 PST)
Andreas Gavrielides
- [AMBER] Questions concerning charges calculated by antechamber (Mon Nov 28 2016 - 04:36:19 PST)
Andreas Tosstorff
- Re: [AMBER] Filename being truncated by pmemd.cuda (Mon Nov 14 2016 - 08:19:56 PST)
- [AMBER] Filename being truncated by pmemd.cuda (Mon Nov 14 2016 - 08:14:03 PST)
- [AMBER] Performance drop for large systems (Tue Nov 08 2016 - 02:11:46 PST)
- [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Thu Nov 03 2016 - 05:15:47 PDT)
Andrew Bostick
- [AMBER] Tools for calculation of interaction energy (Fri Nov 25 2016 - 09:41:26 PST)
Anna Cebrian Prats
- [AMBER] Uridine diphosphate (UDP) - tleap (Fri Nov 04 2016 - 04:58:51 PDT)
anu chandra
- Re: [AMBER] cpptraj RMSD calculation with mismatch residue numbers (Fri Nov 18 2016 - 05:12:32 PST)
- [AMBER] cpptraj RMSD calculation with mismatch residue numbers (Wed Nov 16 2016 - 15:02:04 PST)
Arthi Venkat
- Re: [AMBER] Protein path error (Tue Nov 22 2016 - 02:58:02 PST)
- Re: [AMBER] Protein path error (Tue Nov 22 2016 - 02:23:50 PST)
- [AMBER] Protein path error (Tue Nov 22 2016 - 01:52:18 PST)
asdda asa
- Re: [AMBER] compute RESP charges (Thu Nov 10 2016 - 14:14:00 PST)
- [AMBER] compute RESP charges (Wed Nov 09 2016 - 14:16:45 PST)
Aseel Bala
- [AMBER] ambmask issue (Thu Nov 17 2016 - 10:21:11 PST)
- Re: [AMBER] ambmask issue (Thu Nov 10 2016 - 15:22:18 PST)
- [AMBER] ambmask issue (Thu Nov 10 2016 - 15:08:01 PST)
Atila Petrosian
- [AMBER] MM-GBSA calculation in temperature other than 298 K (Mon Nov 28 2016 - 10:47:36 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K (Sun Nov 20 2016 - 00:52:52 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K (Thu Nov 17 2016 - 05:22:17 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K (Thu Nov 17 2016 - 05:12:09 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K (Wed Nov 16 2016 - 22:46:26 PST)
- [AMBER] MM-GBSA calculation in temperature other than 298.15 K (Tue Nov 15 2016 - 21:42:37 PST)
barsha bharadwaz
- [AMBER] Force field files for ff99IDPs (Wed Nov 30 2016 - 05:04:49 PST)
Batuhan Kav
- Re: [AMBER] dlpc membrane (Mon Nov 14 2016 - 02:36:05 PST)
Beale, John
- [AMBER] Phosphoryated amino acids (Thu Nov 17 2016 - 01:10:30 PST)
Bill Ross
- Re: [AMBER] Error, charge not integral (Wed Nov 23 2016 - 02:59:32 PST)
- Re: [AMBER] simulation running error. (Tue Nov 22 2016 - 21:55:08 PST)
- Re: [AMBER] Issue with addAtomType: Syntax Error (Thu Nov 17 2016 - 13:21:45 PST)
- Re: [AMBER] Issue with addAtomType: Syntax Error (Thu Nov 17 2016 - 12:22:00 PST)
- Re: [AMBER] Phosphoryated amino acids (Thu Nov 17 2016 - 01:25:12 PST)
- Re: [AMBER] Phosphoryated amino acids (Thu Nov 17 2016 - 01:12:58 PST)
- Re: [AMBER] Generation of parameter files of transmembrane protein system via xleap (Mon Nov 14 2016 - 01:21:21 PST)
Brent Krueger
- Re: [AMBER] Obtaining infrared/Raman spectra (Sat Nov 26 2016 - 13:45:07 PST)
- Re: [AMBER] TUTORIAL B5: Simulating the Green Fluorescent Protein -PREPGEN Error (Sun Nov 20 2016 - 06:31:59 PST)
Brian Radak
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD (Tue Nov 29 2016 - 11:34:18 PST)
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD (Tue Nov 29 2016 - 10:56:50 PST)
- [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD (Tue Nov 29 2016 - 10:24:05 PST)
Carlos Simmerling
- Re: [AMBER] Force field files for ff99IDPs (Wed Nov 30 2016 - 05:10:12 PST)
- Re: [AMBER] Etot = ************** with dtt=0.004 (Mon Nov 28 2016 - 09:22:13 PST)
- Re: [AMBER] Etot = ************** with dtt=0.004 (Mon Nov 28 2016 - 08:39:05 PST)
- Re: [AMBER] Dynamic at high temperature (Fri Nov 25 2016 - 10:24:13 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K (Thu Nov 17 2016 - 05:44:36 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K (Thu Nov 17 2016 - 05:18:35 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K (Thu Nov 17 2016 - 04:35:32 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K (Wed Nov 16 2016 - 03:12:43 PST)
- Re: [AMBER] Compatibility of Amber parameters for FF99 and FF14SB forcefields (Tue Nov 15 2016 - 08:25:12 PST)
- Re: [AMBER] MMGBSA decomposition analysis (Fri Nov 11 2016 - 13:27:51 PST)
- Re: [AMBER] RNA backbone dihedral restraints question (Tue Nov 08 2016 - 03:39:27 PST)
- Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? (Mon Nov 07 2016 - 06:10:11 PST)
- Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? (Fri Nov 04 2016 - 08:22:16 PDT)
- Re: [AMBER] RNA backbone dihedral restraints question (Fri Nov 04 2016 - 07:10:31 PDT)
- Re: [AMBER] Can we combine amber and gaff atom types? (Wed Nov 02 2016 - 07:16:29 PDT)
- Re: [AMBER] Simulation of protein in lipid blayer using GB solvation model (Wed Nov 02 2016 - 04:34:49 PDT)
Casalini Tommaso
- Re: [AMBER] MMGBSA: estimating "effective energy" convergence (Wed Nov 02 2016 - 06:44:17 PDT)
case
- Re: [AMBER] Obtaining infrared/Raman spectra (Sat Nov 26 2016 - 05:24:13 PST)
Charles Lin
- Re: [AMBER] cudaMemcpyToSymbol Error (Mon Nov 28 2016 - 01:28:46 PST)
- Re: [AMBER] cudaMemcpyToSymbol Error (Mon Nov 28 2016 - 01:27:35 PST)
- Re: [AMBER] MD under external electric field (Thu Nov 17 2016 - 12:48:12 PST)
- Re: [AMBER] MD under external electric field (Wed Nov 16 2016 - 14:18:46 PST)
- Re: [AMBER] Failed to install mpirun (Thu Nov 03 2016 - 11:39:02 PDT)
- Re: [AMBER] Failed to install mpirun (Thu Nov 03 2016 - 11:35:02 PDT)
Christina Bergonzo
- Re: [AMBER] Converting a PDB Collection to a NetCDF trajectory (Fri Nov 18 2016 - 12:30:48 PST)
cuiyinglukitty
- [AMBER] cudaMemcpyToSymbol Error (Mon Nov 28 2016 - 00:45:48 PST)
Daniel Roe
- Re: [AMBER] cpptraj RMSD calculation with mismatch residue numbers (Wed Nov 30 2016 - 13:07:00 PST)
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD (Wed Nov 30 2016 - 11:18:17 PST)
- Re: [AMBER] Fw: Problems with imaging (Wed Nov 30 2016 - 10:24:32 PST)
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD (Tue Nov 29 2016 - 13:02:44 PST)
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD (Tue Nov 29 2016 - 11:26:29 PST)
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD (Tue Nov 29 2016 - 10:48:38 PST)
- Re: [AMBER] Fw: Problems with imaging (Tue Nov 29 2016 - 05:59:31 PST)
- Re: [AMBER] RMSD for two different MDs (Tue Nov 29 2016 - 05:34:07 PST)
- Re: [AMBER] Questions concerning charges calculated by antechamber (Mon Nov 28 2016 - 05:35:35 PST)
- Re: [AMBER] Regarding integration of my code with CPPTRAJ (Mon Nov 28 2016 - 05:16:03 PST)
- Re: [AMBER] Convert mdcrd files into pbd files (Sun Nov 27 2016 - 11:01:15 PST)
- Re: [AMBER] Extract temperature of a subsytem (Fri Nov 25 2016 - 07:55:40 PST)
- Re: [AMBER] rmsf problem (Wed Nov 23 2016 - 05:06:31 PST)
- Re: [AMBER] Could not find enough velocities in .rst (Wed Nov 23 2016 - 05:02:42 PST)
- Re: [AMBER] Could not find enough velocities in .rst (Tue Nov 22 2016 - 10:28:08 PST)
- Re: [AMBER] Lifetime Analysis in cpptraj (Tue Nov 22 2016 - 06:36:25 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K (Sun Nov 20 2016 - 04:05:06 PST)
- Re: [AMBER] strange format of .rst file (Fri Nov 18 2016 - 08:20:42 PST)
- Re: [AMBER] extracting velocities from rst7 file (Thu Nov 17 2016 - 15:05:18 PST)
- Re: [AMBER] extracting velocities from rst7 file (Thu Nov 17 2016 - 13:00:12 PST)
- Re: [AMBER] ImportError: Could not import Amber Python modules (Thu Nov 17 2016 - 12:40:10 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K (Thu Nov 17 2016 - 08:11:13 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 07:54:11 PST)
- Re: [AMBER] cpptraj: RMSD vs Residue Number. (Fri Nov 11 2016 - 04:10:26 PST)
- Re: [AMBER] PCA trajectories give unrealistic structures (Wed Nov 09 2016 - 12:33:36 PST)
- Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories (Wed Nov 09 2016 - 10:57:59 PST)
- Re: [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) (Tue Nov 08 2016 - 08:17:35 PST)
- Re: [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) (Tue Nov 08 2016 - 06:56:51 PST)
- Re: [AMBER] cpptraj error: 'cluster': Command not found. (Thu Nov 03 2016 - 18:41:21 PDT)
David A Case
- Re: [AMBER] question about calculated density in sander output file (Wed Nov 30 2016 - 11:39:05 PST)
- Re: [AMBER] GlcNAc-UDP problem with frcmod file (Mon Nov 28 2016 - 11:57:23 PST)
- Re: [AMBER] solvate box of long length and short width (Mon Nov 28 2016 - 11:40:47 PST)
- Re: [AMBER] How to create the .off/.lib file of the equilibrated non-aqueous solvent box? (Sun Nov 27 2016 - 13:16:12 PST)
- Re: [AMBER] NAB input file containing first and second structure of RNA (Sun Nov 27 2016 - 13:06:55 PST)
- Re: [AMBER] NAB input file containing first and second structure of RNA (Sun Nov 27 2016 - 09:40:13 PST)
- Re: [AMBER] creating 5' phosphate groups (Sun Nov 27 2016 - 05:44:06 PST)
- Re: [AMBER] recipe for target "parallel" failed (Sat Nov 26 2016 - 17:52:07 PST)
- Re: [AMBER] instal aamber "mpich2" (Fri Nov 25 2016 - 11:29:39 PST)
- Re: [AMBER] Dynamic at high temperature (Fri Nov 25 2016 - 05:44:21 PST)
- Re: [AMBER] Problem with bonds in NAB (Thu Nov 24 2016 - 10:58:09 PST)
- [AMBER] more on the Berendsen thermostat (Wed Nov 23 2016 - 10:44:29 PST)
- Re: [AMBER] DIfferences between thermostats (Tue Nov 22 2016 - 17:36:46 PST)
- Re: [AMBER] Modes associated to the principal components? (Tue Nov 22 2016 - 11:00:16 PST)
- Re: [AMBER] generated correct inputfiles(.iprmtop and .inpcrd ) files (Tue Nov 22 2016 - 05:21:42 PST)
- Re: [AMBER] Fwd: Normal Mode Analysis (Tue Nov 22 2016 - 05:14:38 PST)
- Re: [AMBER] [Amber] Calculating Normal Modes with Restrictions (Tue Nov 22 2016 - 05:11:35 PST)
- [AMBER] creating 5' phosphate groups (Mon Nov 21 2016 - 14:36:13 PST)
- Re: [AMBER] TUTORIAL B5: Simulating the Green Fluorescent Protein -PREPGEN Error (Mon Nov 21 2016 - 06:11:38 PST)
- Re: [AMBER] The parameters for the fully protonated phosphate group (Mon Nov 21 2016 - 06:08:04 PST)
- Re: [AMBER] How to change the dielectric constant in the electrostatic energy term? (Sun Nov 20 2016 - 12:55:47 PST)
- Re: [AMBER] Issue with addAtomType: Syntax Error (Fri Nov 18 2016 - 06:18:05 PST)
- Re: [AMBER] ImportError: Could not import Amber Python modules (Fri Nov 18 2016 - 06:14:38 PST)
- Re: [AMBER] ImportError: Could not import Amber Python modules (Fri Nov 18 2016 - 06:13:46 PST)
- Re: [AMBER] ImportError: Could not import Amber Python modules (Thu Nov 17 2016 - 12:35:53 PST)
- Re: [AMBER] Converting coordinate file generated into pdb format for nuparm (Thu Nov 17 2016 - 05:45:46 PST)
- Re: [AMBER] Phosphoryated amino acids (Thu Nov 17 2016 - 05:39:19 PST)
- Re: [AMBER] ATP Parameters for ff14SB (Wed Nov 16 2016 - 17:38:13 PST)
- Re: [AMBER] GaMD patches to Amber 14 and PME's gridhi parameter (Wed Nov 16 2016 - 06:56:09 PST)
- Re: [AMBER] MD simulation by amber (Wed Nov 16 2016 - 06:00:38 PST)
- Re: [AMBER] dlpc membrane (Tue Nov 15 2016 - 06:29:16 PST)
- Re: [AMBER] Constraints (Tue Nov 15 2016 - 05:19:34 PST)
- Re: [AMBER] Methylated adenine parameter (Tue Nov 15 2016 - 05:15:59 PST)
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB (Tue Nov 15 2016 - 05:04:53 PST)
- Re: [AMBER] covalently bound ligand (Mon Nov 14 2016 - 18:08:18 PST)
- Re: [AMBER] dlpc membrane (Mon Nov 14 2016 - 18:00:17 PST)
- Re: [AMBER] Filename being truncated by pmemd.cuda (Mon Nov 14 2016 - 12:31:53 PST)
- Re: [AMBER] how to neutralize protein when using intrinsic water model (Mon Nov 14 2016 - 08:22:34 PST)
- Re: [AMBER] dlpc membrane (Mon Nov 14 2016 - 08:18:07 PST)
- Re: [AMBER] dlpc membrane (Mon Nov 14 2016 - 04:51:26 PST)
- Re: [AMBER] Generation of parameter files of transmembrane protein system via xleap (Mon Nov 14 2016 - 04:47:21 PST)
- Re: [AMBER] error in antechamber (Fri Nov 11 2016 - 17:14:55 PST)
- Re: [AMBER] length of restraintmask (Fri Nov 11 2016 - 17:09:29 PST)
- Re: [AMBER] Parameters for selenocysteine (Thu Nov 10 2016 - 10:14:14 PST)
- Re: [AMBER] Parameters for selenocysteine (Thu Nov 10 2016 - 07:43:51 PST)
- Re: [AMBER] integer limit for nstlim (Wed Nov 09 2016 - 14:41:58 PST)
- Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories (Wed Nov 09 2016 - 10:32:20 PST)
- Re: [AMBER] Problem with bonds in NAB (Tue Nov 08 2016 - 12:24:35 PST)
- Re: [AMBER] Umbrella simulation with an arbitrary bias potential (Mon Nov 07 2016 - 05:48:07 PST)
- Re: [AMBER] Hello! Distance restraint problems in SANDER (Sat Nov 05 2016 - 17:35:33 PDT)
- Re: [AMBER] Uridine diphosphate (UDP) - tleap (Fri Nov 04 2016 - 10:07:21 PDT)
- [AMBER] Are Intel compilers free for academics? (Fri Nov 04 2016 - 05:08:32 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Fri Nov 04 2016 - 04:58:41 PDT)
- Re: [AMBER] Error in the production of heat.rst file (Thu Nov 03 2016 - 04:48:33 PDT)
- Re: [AMBER] Problem with bonds in NAB (Thu Nov 03 2016 - 04:44:35 PDT)
- Re: [AMBER] Generating parameters of HEME (Wed Nov 02 2016 - 12:35:55 PDT)
David Cerutti
- Re: [AMBER] RMSD for two different MDs (Mon Nov 28 2016 - 13:46:32 PST)
- Re: [AMBER] DIfferences between thermostats (Wed Nov 23 2016 - 14:04:48 PST)
- Re: [AMBER] About multiconformations RESP fitting (Wed Nov 23 2016 - 10:40:17 PST)
- Re: [AMBER] About multiconformations RESP fitting (Wed Nov 23 2016 - 08:27:01 PST)
- Re: [AMBER] DIfferences between thermostats (Wed Nov 23 2016 - 07:48:24 PST)
- Re: [AMBER] DIfferences between thermostats (Tue Nov 22 2016 - 15:40:04 PST)
- Re: [AMBER] DIfferences between thermostats (Tue Nov 22 2016 - 14:42:05 PST)
- Re: [AMBER] 20161121141138.GE88784.scarletmail.rutgers.edu (Mon Nov 21 2016 - 13:20:57 PST)
- Re: [AMBER] The parameters for the fully protonated phosphate group (Mon Nov 21 2016 - 08:55:32 PST)
- Re: [AMBER] The parameters for the fully protonated phosphate group (Sun Nov 20 2016 - 19:22:47 PST)
- Re: [AMBER] ATP Parameters for ff14SB (Wed Nov 16 2016 - 14:07:23 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 08:04:22 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 07:46:06 PST)
- Re: [AMBER] Negative interaction energy between Sodium ions? (Mon Nov 14 2016 - 14:46:16 PST)
- Re: [AMBER] do_debugf changes energy (Thu Nov 03 2016 - 23:43:37 PDT)
- Re: [AMBER] MD simulations, DDR4 2133MHz vs 3200MHz (Thu Nov 03 2016 - 11:23:01 PDT)
- Re: [AMBER] Can we combine amber and gaff atom types? (Thu Nov 03 2016 - 10:13:21 PDT)
- Re: [AMBER] Can we combine amber and gaff atom types? (Wed Nov 02 2016 - 13:44:42 PDT)
Dd H
- Re: [AMBER] The parameters for the fully protonated phosphate group (Sun Nov 20 2016 - 22:56:37 PST)
- Re: [AMBER] Gromber failed. (Thu Nov 03 2016 - 05:31:14 PDT)
- Re: [AMBER] Gromber failed. (Wed Nov 02 2016 - 19:05:40 PDT)
- Re: [AMBER] Gromber failed. (Wed Nov 02 2016 - 18:13:16 PDT)
- Re: [AMBER] Gromber failed. (Wed Nov 02 2016 - 17:56:48 PDT)
- [AMBER] Gromber failed. (Wed Nov 02 2016 - 01:43:51 PDT)
diego.soler.uam.es
- Re: [AMBER] Extract temperature of a subsytem (Fri Nov 25 2016 - 06:15:53 PST)
- [AMBER] Extract temperature of a subsytem (Fri Nov 25 2016 - 03:22:15 PST)
- Re: [AMBER] Umbrella simulation with an arbitrary bias potential (Tue Nov 15 2016 - 02:53:15 PST)
- Re: [AMBER] Potential energy fluctuation of NVT ensemble (Sat Nov 05 2016 - 01:29:38 PDT)
- [AMBER] Umbrella simulation with an arbitrary bias potential (Fri Nov 04 2016 - 03:02:04 PDT)
Dmitry Suplatov
- [AMBER] Converting a PDB Collection to a NetCDF trajectory (Fri Nov 18 2016 - 12:11:41 PST)
DmitryASuplatov
- [AMBER] Compatibility of Amber parameters for FF99 and FF14SB forcefields (Tue Nov 15 2016 - 08:12:45 PST)
Dr. Andreas W. Goetz
- Re: [AMBER] micro iterations in QM/MM optimization. (Wed Nov 02 2016 - 09:28:47 PDT)
Dr. Anselm Horn
- Re: [AMBER] Restraints not working, What Am I doing Wrong? (Tue Nov 15 2016 - 00:45:07 PST)
- Re: [AMBER] recompile Sander suite (Thu Nov 10 2016 - 03:13:48 PST)
- Re: [AMBER] compute RESP charges (Thu Nov 10 2016 - 02:21:31 PST)
Eiros Zamora, Juan
- Re: [AMBER] rmsf problem (Wed Nov 23 2016 - 04:42:39 PST)
- Re: [AMBER] Phosphoryated amino acids (Thu Nov 17 2016 - 02:21:26 PST)
- Re: [AMBER] [mdout_analyzer.py] Problem with OS X El Capitan (Tue Nov 01 2016 - 06:11:45 PDT)
- Re: [AMBER] [mdout_analyzer.py] Problem with OS X El Capitan (Tue Nov 01 2016 - 05:59:46 PDT)
Elvis Martis
- Re: [AMBER] Error for copper atom type (Tue Nov 29 2016 - 21:40:10 PST)
- Re: [AMBER] recipe for target "parallel" failed (Sun Nov 27 2016 - 00:14:51 PST)
- Re: [AMBER] recipe for target "parallel" failed (Sat Nov 26 2016 - 23:13:53 PST)
- Re: [AMBER] recipe for target "parallel" failed (Sat Nov 26 2016 - 10:31:43 PST)
- Re: [AMBER] rmsf problem (Wed Nov 23 2016 - 02:14:08 PST)
- Re: [AMBER] simulation running error. (Tue Nov 22 2016 - 21:41:39 PST)
- Re: [AMBER] Protein path error (Tue Nov 22 2016 - 03:30:32 PST)
- Re: [AMBER] Protein path error (Tue Nov 22 2016 - 02:31:01 PST)
- Re: [AMBER] Protein path error (Tue Nov 22 2016 - 02:08:26 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 07:58:39 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 07:43:39 PST)
- Re: [AMBER] MM-PBSA calculation for HEME-contained protein (Sat Nov 05 2016 - 05:42:36 PDT)
- Re: [AMBER] Error in the production of heat.rst file (Wed Nov 02 2016 - 21:05:26 PDT)
- Re: [AMBER] Error in the production of heat.rst file (Wed Nov 02 2016 - 20:08:18 PDT)
- Re: [AMBER] Generating parameters of HEME (Wed Nov 02 2016 - 16:59:52 PDT)
Eric Lang
- Re: [AMBER] NPT equilibration at constant pH with protonation states allowed to change (Mon Nov 14 2016 - 02:12:46 PST)
- Re: [AMBER] NPT equilibration at constant pH with protonation states allowed to change (Fri Nov 11 2016 - 13:18:50 PST)
- [AMBER] NPT equilibration at constant pH with protonation states allowed to change (Fri Nov 11 2016 - 09:31:56 PST)
- Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories (Wed Nov 09 2016 - 09:16:08 PST)
- [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories (Wed Nov 09 2016 - 03:44:02 PST)
- Re: [AMBER] enhanced sampling conformations by AMD (Wed Nov 09 2016 - 01:50:10 PST)
- Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? (Mon Nov 07 2016 - 03:29:57 PST)
- [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? (Fri Nov 04 2016 - 08:08:55 PDT)
Fabrício Bracht
- Re: [AMBER] Error, charge not integral (Wed Nov 23 2016 - 03:29:12 PST)
- Re: [AMBER] Error, charge not integral (Wed Nov 23 2016 - 02:39:39 PST)
- [AMBER] Error, charge not integral (Wed Nov 23 2016 - 02:26:46 PST)
- [AMBER] Constant pH charge set (Thu Nov 10 2016 - 06:05:42 PST)
- Re: [AMBER] MCPB problems (Tue Nov 01 2016 - 09:49:35 PDT)
- Re: [AMBER] MCPB problems (Tue Nov 01 2016 - 09:28:47 PDT)
- [AMBER] MCPB problems (Tue Nov 01 2016 - 07:58:42 PDT)
Feng Pan
- Re: [AMBER] Optimal values for harm and output_freq in SMD (Tue Nov 29 2016 - 17:22:30 PST)
- Re: [AMBER] Optimal values for harm and output_freq in SMD (Mon Nov 28 2016 - 18:16:18 PST)
- Re: [AMBER] Optimal values for harm and output_freq in SMD (Thu Nov 24 2016 - 10:55:04 PST)
- Re: [AMBER] No output_file during SMD with LCOD (Thu Nov 17 2016 - 09:03:08 PST)
- Re: [AMBER] Umbrella simulation with an arbitrary bias potential (Mon Nov 07 2016 - 11:44:10 PST)
FyD
- Re: [AMBER] About multiconformations RESP fitting (Fri Nov 25 2016 - 00:07:34 PST)
- Re: [AMBER] About multiconformations RESP fitting (Thu Nov 24 2016 - 02:32:38 PST)
- Re: [AMBER] covalently bound ligand (Mon Nov 14 2016 - 23:36:17 PST)
- Re: [AMBER] Uridine diphosphate (UDP) - tleap (Wed Nov 09 2016 - 02:58:18 PST)
Geoffrey Gray
- Re: [AMBER] DIfferences between thermostats (Tue Nov 22 2016 - 14:09:32 PST)
- Re: [AMBER] DIfferences between thermostats (Tue Nov 22 2016 - 11:38:30 PST)
George Tzotzos
- Re: [AMBER] MMGBSA decomposition analysis (Fri Nov 11 2016 - 13:30:46 PST)
- [AMBER] MMGBSA decomposition analysis (Fri Nov 11 2016 - 13:16:41 PST)
- Re: [AMBER] MMGBSA: estimating "effective energy" convergence (Wed Nov 02 2016 - 07:30:42 PDT)
- [AMBER] MMGBSA: estimating "effective energy" convergence (Wed Nov 02 2016 - 06:38:36 PDT)
giulia palermo
- Re: [AMBER] extracting velocities from rst7 file (Thu Nov 17 2016 - 13:39:07 PST)
- [AMBER] extracting velocities from rst7 file (Thu Nov 17 2016 - 10:55:59 PST)
- [AMBER] AMBER FF for intrinsically disordered protein (Tue Nov 08 2016 - 19:53:35 PST)
Gulsevin,Alican
- [AMBER] PCA trajectories give unrealistic structures (Wed Nov 09 2016 - 08:06:43 PST)
Gustavo Seabra
- Re: [AMBER] Extract temperature of a subsytem (Fri Nov 25 2016 - 05:24:19 PST)
- Re: [AMBER] DIfferences between thermostats (Thu Nov 24 2016 - 05:23:58 PST)
- Re: [AMBER] DIfferences between thermostats (Thu Nov 24 2016 - 04:58:43 PST)
- Re: [AMBER] DIfferences between thermostats (Wed Nov 23 2016 - 13:22:32 PST)
- Re: [AMBER] DIfferences between thermostats (Wed Nov 23 2016 - 08:45:47 PST)
- Re: [AMBER] DIfferences between thermostats (Tue Nov 22 2016 - 12:13:11 PST)
- Re: [AMBER] DIfferences between thermostats (Tue Nov 22 2016 - 11:38:06 PST)
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB (Wed Nov 16 2016 - 04:26:41 PST)
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB (Thu Nov 10 2016 - 09:44:45 PST)
Hai Nguyen
- Re: [AMBER] mdfil: Error unknown flag: pdb_wat.prmtop (Wed Nov 30 2016 - 15:33:47 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298 K (Mon Nov 28 2016 - 11:13:06 PST)
- Re: [AMBER] Regarding integration of my code with CPPTRAJ (Sun Nov 27 2016 - 21:47:06 PST)
- Re: [AMBER] Convert prm into prmtop - from NAMD to AMBER (Mon Nov 21 2016 - 11:29:31 PST)
- Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) (Fri Nov 18 2016 - 17:09:35 PST)
- Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) (Fri Nov 18 2016 - 13:06:33 PST)
- Re: [AMBER] Converting a PDB Collection to a NetCDF trajectory (Fri Nov 18 2016 - 12:19:33 PST)
- Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) (Fri Nov 18 2016 - 10:30:01 PST)
- Re: [AMBER] extracting velocities from rst7 file (Thu Nov 17 2016 - 12:58:09 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 08:11:24 PST)
- Re: [AMBER] Problem with Parmed-generated chamber prmtop (Tue Nov 15 2016 - 18:50:32 PST)
- Re: [AMBER] mm_pbsa.pl error: Found unknown atflg DC (Tue Nov 15 2016 - 18:42:37 PST)
- Re: [AMBER] MD simulation by amber (Tue Nov 15 2016 - 18:40:12 PST)
- Re: [AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day (Tue Nov 15 2016 - 07:13:20 PST)
- Re: [AMBER] ambmask issue (Thu Nov 10 2016 - 15:11:29 PST)
- Re: [AMBER] Error in the production of heat.rst file (Thu Nov 03 2016 - 17:55:16 PDT)
- Re: [AMBER] RESP routine not found (Thu Nov 03 2016 - 09:52:52 PDT)
- Re: [AMBER] Gromber failed. (Wed Nov 02 2016 - 18:00:20 PDT)
- Re: [AMBER] Generating parameters of HEME (Wed Nov 02 2016 - 10:48:15 PDT)
- Re: [AMBER] Problem installing Amber 16 on mac OS El Capitan (Wed Nov 02 2016 - 07:14:09 PDT)
Haining Liu
- [AMBER] RMSD for two different MDs (Mon Nov 28 2016 - 12:49:02 PST)
Hannes Loeffler
- Re: [AMBER] GlcNAc-UDP problem with frcmod file (Fri Nov 25 2016 - 03:28:02 PST)
- Re: [AMBER] Error in running FEW calculations (Wed Nov 09 2016 - 00:51:25 PST)
- Re: [AMBER] Error in running FEW calculations (Wed Nov 09 2016 - 00:39:31 PST)
- Re: [AMBER] Error in running FEW calculations (Wed Nov 09 2016 - 00:21:39 PST)
Hector A. Baldoni
- Re: [AMBER] MD under external electric field (Thu Nov 17 2016 - 05:56:13 PST)
- [AMBER] MD under external electric field (Wed Nov 16 2016 - 13:36:05 PST)
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB (Wed Nov 16 2016 - 05:06:59 PST)
Hirdesh Kumar
- Re: [AMBER] Issue with the gaff parameters for "nh" atom type (Wed Nov 30 2016 - 11:13:35 PST)
Hyun
- [AMBER] selection of the residues when using MM-GBSA (Wed Nov 30 2016 - 08:38:08 PST)
Ibrahim Said
- [AMBER] recompile Sander suite (Thu Nov 10 2016 - 02:56:34 PST)
Ignacio J. General
- [AMBER] length of restraintmask (Fri Nov 11 2016 - 09:51:50 PST)
Imma Speciale
- [AMBER] Dynamic at high temperature (Fri Nov 25 2016 - 03:49:01 PST)
- Re: [AMBER] Fwd: Normal Mode Analysis (Tue Nov 22 2016 - 06:33:07 PST)
- Re: [AMBER] Fwd: Normal Mode Analysis (Tue Nov 22 2016 - 02:42:02 PST)
- [AMBER] Fwd: Normal Mode Analysis (Thu Nov 17 2016 - 05:47:45 PST)
Jason Swails
- Re: [AMBER] selection of the residues when using MM-GBSA (Wed Nov 30 2016 - 13:31:39 PST)
- Re: [AMBER] MCPB.py and MMPBSA issue (Tue Nov 29 2016 - 09:17:33 PST)
- Re: [AMBER] Problem with Parmed-generated chamber prmtop (Wed Nov 23 2016 - 08:47:58 PST)
- Re: [AMBER] Modes associated to the principal components? (Tue Nov 22 2016 - 09:26:31 PST)
- Re: [AMBER] Problem with Parmed-generated chamber prmtop (Fri Nov 18 2016 - 16:49:07 PST)
- Re: [AMBER] Problem with Parmed-generated chamber prmtop (Fri Nov 18 2016 - 11:45:19 PST)
- Re: [AMBER] strange format of .rst file (Fri Nov 18 2016 - 09:13:43 PST)
- Re: [AMBER] ImportError: Could not import Amber Python modules (Thu Nov 17 2016 - 13:23:48 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K (Thu Nov 17 2016 - 09:55:37 PST)
- Re: [AMBER] Help Constant pH MD calculations (Tue Nov 15 2016 - 11:24:25 PST)
- Re: [AMBER] Constraints (Tue Nov 15 2016 - 11:20:07 PST)
- Re: [AMBER] NPT equilibration at constant pH with protonation states allowed to change (Fri Nov 11 2016 - 09:39:05 PST)
- Re: [AMBER] Constant pH charge set (Thu Nov 10 2016 - 06:22:12 PST)
- Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? (Fri Nov 04 2016 - 12:52:26 PDT)
- Re: [AMBER] Gromber failed. (Thu Nov 03 2016 - 03:18:04 PDT)
- Re: [AMBER] Gromber failed. (Wed Nov 02 2016 - 05:14:09 PDT)
- Re: [AMBER] [mdout_analyzer.py] Problem with OS X El Capitan (Tue Nov 01 2016 - 06:13:49 PDT)
jinfeng liu
- [AMBER] The parameters for the fully protonated phosphate group (Sun Nov 20 2016 - 18:45:31 PST)
Joan Torras
- [AMBER] Software announcement: Release of PUPIL 3.1 (Wed Nov 02 2016 - 13:33:54 PDT)
jojartb.jgypk.u-szeged.hu
- Re: [AMBER] dlpc membrane (Mon Nov 14 2016 - 21:17:49 PST)
- Re: [AMBER] dlpc membrane (Mon Nov 14 2016 - 09:26:22 PST)
- Re: [AMBER] dlpc membrane (Mon Nov 14 2016 - 08:41:16 PST)
- Re: [AMBER] dlpc membrane (Mon Nov 14 2016 - 05:38:28 PST)
- Re: [AMBER] dlpc membrane (Mon Nov 14 2016 - 03:05:17 PST)
- [AMBER] dlpc membrane (Mon Nov 14 2016 - 01:45:03 PST)
Jon Mujika
- [AMBER] MCPB.py error in Step 2 (Thu Nov 10 2016 - 03:25:11 PST)
Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] GaMD patches to Amber 14 and PME's gridhi parameter (Wed Nov 16 2016 - 07:36:06 PST)
- [AMBER] GaMD patches to Amber 14 and PME's gridhi parameter (Wed Nov 16 2016 - 06:07:03 PST)
- Re: [AMBER] RNA backbone dihedral restraints question (Fri Nov 04 2016 - 07:41:00 PDT)
- [AMBER] RNA backbone dihedral restraints question (Fri Nov 04 2016 - 07:05:25 PDT)
Kat G
- [AMBER] enhanced sampling conformations by AMD (Mon Nov 07 2016 - 09:03:29 PST)
Korey M Reid
- Re: [AMBER] Issue with addAtomType: Syntax Error (Fri Nov 18 2016 - 13:57:34 PST)
- Re: [AMBER] Issue with addAtomType: Syntax Error (Thu Nov 17 2016 - 13:01:23 PST)
- [AMBER] Issue with addAtomType: Syntax Error (Thu Nov 17 2016 - 12:14:36 PST)
Kshatresh Dutta Dubey
- [AMBER] Methylated adenine parameter (Tue Nov 15 2016 - 02:45:07 PST)
Lachele Foley
- Re: [AMBER] GlcNAc-UDP problem with frcmod file (Mon Nov 28 2016 - 23:40:16 PST)
- Re: [AMBER] Error, charge not integral (Wed Nov 23 2016 - 03:01:13 PST)
Lara rajam
- Re: [AMBER] solvate box of long length and short width (Mon Nov 28 2016 - 12:22:12 PST)
- [AMBER] solvate box of long length and short width (Mon Nov 28 2016 - 06:58:31 PST)
Magno .
- [AMBER] compatibility (Wed Nov 16 2016 - 10:13:16 PST)
Mahmood Jasim
- Re: [AMBER] MCPB.py (Thu Nov 03 2016 - 03:02:59 PDT)
Mahrukh Imtiaz
- Re: [AMBER] Distorsion in water box size and shape (Wed Nov 23 2016 - 22:13:14 PST)
- [AMBER] Generation of parameter files of transmembrane protein system via xleap (Mon Nov 14 2016 - 01:05:39 PST)
Marc van der Kamp
- Re: [AMBER] Problem with Parmed-generated chamber prmtop (Thu Nov 24 2016 - 02:34:37 PST)
- Re: [AMBER] DIfferences between thermostats (Wed Nov 23 2016 - 07:53:48 PST)
- Re: [AMBER] Problem with Parmed-generated chamber prmtop (Fri Nov 18 2016 - 14:39:40 PST)
- [AMBER] Problem with Parmed-generated chamber prmtop (Thu Nov 10 2016 - 07:01:48 PST)
Marcelo Depólo
- [AMBER] RESP routine not found (Thu Nov 03 2016 - 05:09:32 PDT)
Marek Maly
- Re: [AMBER] problem with MMPBSApy in Amber 16 (Tue Nov 01 2016 - 15:20:40 PDT)
- Re: [AMBER] problem with MMPBSApy in Amber 16 (Tue Nov 01 2016 - 12:14:55 PDT)
- Re: [AMBER] problem with MMPBSApy in Amber 16 (Tue Nov 01 2016 - 10:36:24 PDT)
- [AMBER] problem with MMPBSApy in Amber 16 (Tue Nov 01 2016 - 08:54:04 PDT)
Marion, Antoine
- Re: [AMBER] About multiconformations RESP fitting (Fri Nov 25 2016 - 01:40:07 PST)
- Re: [AMBER] About multiconformations RESP fitting (Thu Nov 24 2016 - 05:38:45 PST)
- Re: [AMBER] About multiconformations RESP fitting (Thu Nov 24 2016 - 01:06:32 PST)
- Re: [AMBER] About multiconformations RESP fitting (Wed Nov 23 2016 - 09:29:29 PST)
- [AMBER] About multiconformations RESP fitting (Wed Nov 23 2016 - 07:39:16 PST)
Mark Waterhouse [RPG]
- Re: [AMBER] Fw: Problems with imaging (Wed Nov 30 2016 - 01:08:00 PST)
- [AMBER] Fw: Problems with imaging (Mon Nov 28 2016 - 12:49:09 PST)
Markowska
- Re: [AMBER] DIfferences between thermostats (Thu Nov 24 2016 - 05:10:43 PST)
- Re: [AMBER] DIfferences between thermostats (Wed Nov 23 2016 - 14:45:17 PST)
- Re: [AMBER] DIfferences between thermostats (Wed Nov 23 2016 - 13:26:54 PST)
- Re: [AMBER] more on the Berendsen thermostat (Wed Nov 23 2016 - 11:07:59 PST)
- Re: [AMBER] DIfferences between thermostats (Wed Nov 23 2016 - 10:54:16 PST)
- Re: [AMBER] DIfferences between thermostats (Wed Nov 23 2016 - 00:14:47 PST)
- Re: [AMBER] DIfferences between thermostats (Tue Nov 22 2016 - 12:06:24 PST)
- [AMBER] DIfferences between thermostats (Tue Nov 22 2016 - 11:31:18 PST)
Michael Shokhen
- Re: [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) (Tue Nov 08 2016 - 07:38:40 PST)
- [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) (Tue Nov 08 2016 - 05:28:06 PST)
Miguel Rivera
- Re: [AMBER] Error in running FEW calculations (Wed Nov 09 2016 - 00:44:34 PST)
- Re: [AMBER] Error in running FEW calculations (Wed Nov 09 2016 - 00:26:49 PST)
- [AMBER] Error in running FEW calculations (Tue Nov 08 2016 - 12:50:23 PST)
Mohaddeseh Habibzadeh
- Re: [AMBER] NAB input file containing first and second structure of RNA (Mon Nov 28 2016 - 01:32:20 PST)
- Re: [AMBER] creating 5' phosphate groups (Sun Nov 27 2016 - 10:05:57 PST)
- Re: [AMBER] NAB input file containing first and second structure of RNA (Sun Nov 27 2016 - 09:56:59 PST)
- Re: [AMBER] creating 5' phosphate groups (Sun Nov 27 2016 - 03:12:22 PST)
- Re: [AMBER] recipe for target "parallel" failed (Sun Nov 27 2016 - 00:07:24 PST)
- Re: [AMBER] recipe for target "parallel" failed (Sat Nov 26 2016 - 23:03:56 PST)
- [AMBER] NAB input file containing first and second structure of RNA (Sat Nov 26 2016 - 22:56:16 PST)
- Re: [AMBER] recipe for target "parallel" failed (Sat Nov 26 2016 - 22:38:56 PST)
- Re: [AMBER] recipe for target "parallel" failed (Sat Nov 26 2016 - 11:03:35 PST)
- [AMBER] recipe for target "parallel" failed (Sat Nov 26 2016 - 10:08:58 PST)
- [AMBER] cap the 5' phosphate of a RNA (Mon Nov 21 2016 - 11:48:23 PST)
MOHD HOMAIDUR RAHMAN
- [AMBER] Lifetime Analysis in cpptraj (Mon Nov 21 2016 - 11:20:06 PST)
muhammad tahir ayub
- [AMBER] Hydrophobic and covalent interactions bond length and stability (Wed Nov 23 2016 - 21:46:04 PST)
Neale, Christopher Andrew
- [AMBER] integer limit for nstlim (Wed Nov 09 2016 - 14:14:12 PST)
- [AMBER] can not find chamber in amber16? (Fri Nov 04 2016 - 09:25:51 PDT)
Neha Gandhi
- [AMBER] AMBER Materials modelling- periodic image (Sun Nov 27 2016 - 21:41:46 PST)
- Re: [AMBER] Phosphoryated amino acids (Thu Nov 17 2016 - 01:35:20 PST)
- [AMBER] log file in aMD (Wed Nov 09 2016 - 02:50:12 PST)
- Re: [AMBER] AMBER FF for intrinsically disordered protein (Tue Nov 08 2016 - 19:56:46 PST)
- [AMBER] number of cpus in parallel GPU jobs (Tue Nov 08 2016 - 17:42:03 PST)
Nehad Elsalamouny
- [AMBER] error in antechamber (Fri Nov 11 2016 - 16:10:17 PST)
Nhai
- Re: [AMBER] Etot = ************** with dtt=0.004 (Mon Nov 28 2016 - 10:01:38 PST)
- Re: [AMBER] Convert mdcrd files into pbd files (Fri Nov 25 2016 - 14:52:28 PST)
- Re: [AMBER] Tools for calculation of interaction energy (Fri Nov 25 2016 - 12:57:48 PST)
- Re: [AMBER] instal aamber "mpich2" (Fri Nov 25 2016 - 09:37:15 PST)
- Re: [AMBER] Extract temperature of a subsytem (Fri Nov 25 2016 - 07:54:46 PST)
- Re: [AMBER] DIfferences between thermostats (Wed Nov 23 2016 - 07:57:59 PST)
- Re: [AMBER] aMD with dt=0.004 (Wed Nov 23 2016 - 07:47:16 PST)
- Re: [AMBER] extracting velocities from rst7 file (Thu Nov 17 2016 - 14:54:24 PST)
- Re: [AMBER] ImportError: Could not import Amber Python modules (Thu Nov 17 2016 - 11:48:37 PST)
- Re: [AMBER] ImportError: Could not import Amber Python modules (Thu Nov 17 2016 - 09:47:27 PST)
- Re: [AMBER] creating parameters for integrins (Thu Nov 17 2016 - 09:44:00 PST)
- Re: [AMBER] Fwd: Normal Mode Analysis (Thu Nov 17 2016 - 06:54:09 PST)
- Re: [AMBER] Converting coordinate file generated into pdb format for nuparm (Thu Nov 17 2016 - 06:44:11 PST)
- Re: [AMBER] cpptraj RMSD calculation with mismatch residue numbers (Wed Nov 16 2016 - 15:26:16 PST)
- Re: [AMBER] dlpc membrane (Mon Nov 14 2016 - 08:55:48 PST)
- Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories (Wed Nov 09 2016 - 07:07:40 PST)
- Re: [AMBER] can not find chamber in amber16? (Fri Nov 04 2016 - 09:34:04 PDT)
- Re: [AMBER] Gromber failed. (Wed Nov 02 2016 - 18:58:03 PDT)
Niel Henriksen
- Re: [AMBER] ImportError: Could not import Amber Python modules (Thu Nov 17 2016 - 13:28:36 PST)
- Re: [AMBER] Potential energy fluctuation of NVT ensemble (Fri Nov 04 2016 - 17:25:22 PDT)
Nikhil Chowdary
- [AMBER] Regarding integration of my code with CPPTRAJ (Sun Nov 27 2016 - 21:35:46 PST)
Nikolay N. Kuzmich
- [AMBER] Failed to install mpirun (Thu Nov 03 2016 - 10:58:30 PDT)
- [AMBER] MD simulations, DDR4 2133MHz vs 3200MHz (Thu Nov 03 2016 - 10:53:17 PDT)
- [AMBER] Simulation of protein in lipid blayer using GB solvation model (Wed Nov 02 2016 - 03:49:34 PDT)
- [AMBER] The ultimate temperature is 11K instead of 100K in heating simulation (Tue Nov 01 2016 - 10:34:22 PDT)
Ol Sta
- [AMBER] Constraints (Fri Nov 11 2016 - 06:34:07 PST)
Oliver Emil Skytte Glue
- Re: [AMBER] Negative interaction energy between Sodium ions? (Mon Nov 14 2016 - 14:29:17 PST)
Paul Meister
- [AMBER] Parameters for selenocysteine (Thu Nov 10 2016 - 06:06:54 PST)
Pengfei Li
- Re: [AMBER] AMBER Materials modelling- periodic image (Mon Nov 28 2016 - 13:17:21 PST)
- Re: [AMBER] MCPB.py and MMPBSA issue (Mon Nov 28 2016 - 13:09:46 PST)
- Re: [AMBER] is it possible to run aMD in implicit water model? (Tue Nov 22 2016 - 16:58:16 PST)
- Re: [AMBER] is it possible to run aMD in implicit water model? (Tue Nov 22 2016 - 12:54:33 PST)
- Re: [AMBER] Query regarding the MCPB.py workflow (Mon Nov 21 2016 - 14:27:34 PST)
- Re: [AMBER] Query regarding the MCPB.py workflow (Wed Nov 16 2016 - 17:07:22 PST)
- Re: [AMBER] Query regarding the MCPB.py workflow (Wed Nov 16 2016 - 17:05:31 PST)
- Re: [AMBER] MCPB.py error in Step 2 (Fri Nov 11 2016 - 09:52:42 PST)
- Re: [AMBER] Quenstions about pmemd.cuda.MPI (Thu Nov 10 2016 - 17:48:11 PST)
- Re: [AMBER] MCPB.py (Tue Nov 08 2016 - 10:53:11 PST)
- Re: [AMBER] Quenstions about pmemd.cuda.MPI (Sun Nov 06 2016 - 22:27:21 PST)
- [AMBER] Quenstions about pmemd.cuda.MPI (Thu Nov 03 2016 - 20:20:41 PDT)
- Re: [AMBER] MCPB problems (Wed Nov 02 2016 - 19:13:42 PDT)
- Re: [AMBER] MCPB problems (Tue Nov 01 2016 - 09:16:21 PDT)
Prajwal Nandekar
- [AMBER] Issue with the gaff parameters for "nh" atom type (Wed Nov 30 2016 - 05:58:45 PST)
Preeti Pandey
- [AMBER] MMPBSA Calculation (Mon Nov 21 2016 - 08:49:43 PST)
Ramin Ekhteiari
- [AMBER] MM-PBSA calculation for HEME-contained protein (Sat Nov 05 2016 - 05:14:47 PDT)
- [AMBER] Generating parameters of HEME (Wed Nov 02 2016 - 10:32:11 PDT)
Ray Luo
- Re: [AMBER] problem with MMPBSApy in Amber 16 (Tue Nov 01 2016 - 14:34:01 PDT)
- Re: [AMBER] problem with MMPBSApy in Amber 16 (Tue Nov 01 2016 - 13:29:22 PDT)
- Re: [AMBER] problem with MMPBSApy in Amber 16 (Tue Nov 01 2016 - 10:49:36 PDT)
- Re: [AMBER] mmpbsa error (Tue Nov 01 2016 - 10:35:45 PDT)
- Re: [AMBER] problem with MMPBSApy in Amber 16 (Tue Nov 01 2016 - 09:14:50 PDT)
Robin Betz
- Re: [AMBER] Paramfit for multiple molecules (Mon Nov 28 2016 - 15:47:05 PST)
Roitberg,Adrian E
- Re: [AMBER] Etot = ************** with dtt=0.004 (Mon Nov 28 2016 - 08:47:43 PST)
- Re: [AMBER] Constraints (Tue Nov 15 2016 - 06:21:01 PST)
Ross Walker
- Re: [AMBER] Etot = ************** with dtt=0.004 (Mon Nov 28 2016 - 12:21:35 PST)
- Re: [AMBER] cudaMemcpyToSymbol Error (Mon Nov 28 2016 - 05:46:45 PST)
- Re: [AMBER] Problem to submit a pH-REMD on a GPU node (Fri Nov 25 2016 - 07:57:16 PST)
- Re: [AMBER] Quenstions about pmemd.cuda.MPI (Thu Nov 10 2016 - 18:33:32 PST)
- Re: [AMBER] CUDA version for Amber14 (Thu Nov 10 2016 - 06:57:27 PST)
- Re: [AMBER] number of cpus in parallel GPU jobs (Tue Nov 08 2016 - 19:08:08 PST)
- Re: [AMBER] Performance drop for large systems (Tue Nov 08 2016 - 05:48:08 PST)
- Re: [AMBER] Quenstions about pmemd.cuda.MPI (Mon Nov 07 2016 - 06:29:29 PST)
- Re: [AMBER] Quenstions about pmemd.cuda.MPI (Thu Nov 03 2016 - 20:48:16 PDT)
- Re: [AMBER] The ultimate temperature is 11K instead of 100K in heating simulation (Tue Nov 01 2016 - 10:38:51 PDT)
Ruth Helena Tichauer
- Re: [AMBER] Optimal values for harm and output_freq in SMD (Wed Nov 30 2016 - 01:32:31 PST)
- Re: [AMBER] Optimal values for harm and output_freq in SMD (Tue Nov 29 2016 - 07:59:07 PST)
- Re: [AMBER] Optimal values for harm and output_freq in SMD (Fri Nov 25 2016 - 03:47:37 PST)
- [AMBER] Optimal values for harm and output_freq in SMD (Thu Nov 24 2016 - 03:34:04 PST)
- Re: [AMBER] Could not find enough velocities in .rst (Wed Nov 23 2016 - 05:33:33 PST)
- Re: [AMBER] Could not find enough velocities in .rst (Wed Nov 23 2016 - 01:52:23 PST)
- [AMBER] Could not find enough velocities in .rst (Tue Nov 22 2016 - 09:21:32 PST)
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB (Fri Nov 18 2016 - 07:16:57 PST)
- Re: [AMBER] No output_file during SMD with LCOD (Fri Nov 18 2016 - 07:04:06 PST)
- [AMBER] No output_file during SMD with LCOD (Thu Nov 17 2016 - 02:45:47 PST)
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB (Wed Nov 16 2016 - 04:32:01 PST)
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB (Tue Nov 15 2016 - 05:16:42 PST)
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB (Tue Nov 15 2016 - 01:47:37 PST)
- [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB (Thu Nov 10 2016 - 06:07:29 PST)
- Re: [AMBER] cpptraj error: 'cluster': Command not found. (Fri Nov 04 2016 - 01:51:17 PDT)
- [AMBER] cpptraj error: 'cluster': Command not found. (Thu Nov 03 2016 - 08:59:45 PDT)
- Re: [AMBER] Problem installing Amber 16 on mac OS El Capitan (Wed Nov 02 2016 - 08:13:25 PDT)
- [AMBER] Problem installing Amber 16 on mac OS El Capitan (Wed Nov 02 2016 - 06:32:15 PDT)
Saman Yousuf ali
- Re: [AMBER] simulation running error. (Tue Nov 22 2016 - 22:02:30 PST)
- Re: [AMBER] simulation running error. (Tue Nov 22 2016 - 21:49:50 PST)
- [AMBER] simulation running error. (Tue Nov 22 2016 - 21:31:15 PST)
- [AMBER] cpptraj: RMSD vs Residue Number. (Fri Nov 11 2016 - 00:48:23 PST)
Samuel Bowerman
- Re: [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) (Tue Nov 08 2016 - 06:23:31 PST)
Sepideh Jafari
- Re: [AMBER] instal aamber "mpich2" (Fri Nov 25 2016 - 09:51:54 PST)
- [AMBER] instal aamber "mpich2" (Fri Nov 25 2016 - 09:23:44 PST)
- [AMBER] rmsf problem (Wed Nov 23 2016 - 02:07:27 PST)
Sergey Samsonov
- [AMBER] GIST: convergence of the translational entropy term (Fri Nov 11 2016 - 06:28:26 PST)
Shreeramesh
- [AMBER] Error for copper atom type (Tue Nov 29 2016 - 18:26:02 PST)
Sofia Vasilakaki
- [AMBER] CUDA version for Amber14 (Wed Nov 09 2016 - 14:17:39 PST)
Sonia Romero
- [AMBER] GlcNAc-UDP problem with frcmod file (Fri Nov 25 2016 - 02:15:41 PST)
Sonia Ziada
- [AMBER] Targeted molecular dynamics on GPU (Mon Nov 14 2016 - 07:14:34 PST)
Stacyann Nelson
- Re: [AMBER] Error in the production of heat.rst file (Thu Nov 03 2016 - 17:20:51 PDT)
- Re: [AMBER] Error in the production of heat.rst file (Wed Nov 02 2016 - 20:44:47 PDT)
- [AMBER] Error in the production of heat.rst file (Wed Nov 02 2016 - 17:32:33 PDT)
Steven Ramsey
- Re: [AMBER] GIST: convergence of the translational entropy term (Fri Nov 11 2016 - 08:43:15 PST)
Stevens, David Ryan
- [AMBER] ATP Parameters for ff14SB (Wed Nov 16 2016 - 13:57:21 PST)
Sven Hackbusch
- [AMBER] Paramfit for multiple molecules (Tue Nov 22 2016 - 15:59:22 PST)
tanfei777.sina.cn
- [AMBER] Hello! Distance restraint problems in SANDER (Sat Nov 05 2016 - 01:11:18 PDT)
Taylor, Miles
- [AMBER] 20161121141138.GE88784.scarletmail.rutgers.edu (Wed Nov 23 2016 - 07:56:48 PST)
- [AMBER] 20161121141138.GE88784.scarletmail.rutgers.edu (Mon Nov 21 2016 - 12:36:36 PST)
- [AMBER] TUTORIAL B5: Simulating the Green Fluorescent Protein -PREPGEN Error (Sat Nov 19 2016 - 16:50:20 PST)
Thakur, Abhishek
- Re: [AMBER] RMSD for two different MDs (Mon Nov 28 2016 - 13:27:53 PST)
- Re: [AMBER] Etot = ************** with dtt=0.004 (Mon Nov 28 2016 - 09:45:25 PST)
- Re: [AMBER] Etot = ************** with dtt=0.004 (Mon Nov 28 2016 - 09:15:12 PST)
- Re: [AMBER] Etot = ************** with dtt=0.004 (Mon Nov 28 2016 - 09:06:21 PST)
- Re: [AMBER] Etot = ************** with dtt=0.004 (Mon Nov 28 2016 - 08:43:09 PST)
- [AMBER] Etot = ************** with dtt=0.004 (Mon Nov 28 2016 - 08:29:40 PST)
- [AMBER] aMD with dt=0.004 (Wed Nov 23 2016 - 06:53:34 PST)
- Re: [AMBER] is it possible to run aMD in implicit water model? (Tue Nov 22 2016 - 17:46:36 PST)
- Re: [AMBER] is it possible to run aMD in implicit water model? (Tue Nov 22 2016 - 14:36:52 PST)
- [AMBER] is it possible to run aMD in implicit water model? (Tue Nov 22 2016 - 12:51:26 PST)
- [AMBER] implicit water model in aMD (Mon Nov 21 2016 - 13:45:04 PST)
- Re: [AMBER] strange format of .rst file (Fri Nov 18 2016 - 09:04:15 PST)
- [AMBER] strange format of .rst file (Fri Nov 18 2016 - 07:53:41 PST)
- Re: [AMBER] ImportError: Could not import Amber Python modules (Thu Nov 17 2016 - 12:52:31 PST)
- Re: [AMBER] ImportError: Could not import Amber Python modules (Thu Nov 17 2016 - 11:51:06 PST)
- Re: [AMBER] ImportError: Could not import Amber Python modules (Thu Nov 17 2016 - 11:02:40 PST)
- [AMBER] ImportError: Could not import Amber Python modules (Thu Nov 17 2016 - 09:42:56 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 11:02:17 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 10:31:28 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 08:41:02 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 07:57:42 PST)
- Re: [AMBER] HMassRepartition (Wed Nov 16 2016 - 07:55:45 PST)
- [AMBER] HMassRepartition (Wed Nov 16 2016 - 07:38:23 PST)
- Re: [AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day (Tue Nov 15 2016 - 09:12:37 PST)
- [AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day (Tue Nov 15 2016 - 07:01:41 PST)
- [AMBER] how to neutralize protein when using intrinsic water model (Mon Nov 14 2016 - 08:00:46 PST)
The Cromicus Productions
- [AMBER] Obtaining infrared/Raman spectra (Sat Nov 26 2016 - 00:36:22 PST)
- [AMBER] Convert mdcrd files into pbd files (Fri Nov 25 2016 - 14:47:00 PST)
- Re: [AMBER] Modes associated to the principal components? (Tue Nov 22 2016 - 10:52:36 PST)
- [AMBER] Modes associated to the principal components? (Tue Nov 22 2016 - 06:54:45 PST)
- Re: [AMBER] [Amber] Calculating Normal Modes with Restrictions (Tue Nov 22 2016 - 06:49:26 PST)
- Re: [AMBER] [Amber] Calculating Normal Modes with Restrictions (Tue Nov 22 2016 - 06:30:50 PST)
- Re: [AMBER] Fwd: Normal Mode Analysis (Tue Nov 22 2016 - 06:29:34 PST)
- [AMBER] [Amber] Calculating Normal Modes with Restrictions (Mon Nov 21 2016 - 17:00:26 PST)
- Re: [AMBER] Convert prm into prmtop - from NAMD to AMBER (Mon Nov 21 2016 - 11:43:44 PST)
- Re: [AMBER] Convert prm into prmtop - from NAMD to AMBER (Mon Nov 21 2016 - 11:36:27 PST)
- [AMBER] Convert prm into prmtop - from NAMD to AMBER (Mon Nov 21 2016 - 11:21:43 PST)
- Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) (Fri Nov 18 2016 - 17:12:39 PST)
- Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) (Fri Nov 18 2016 - 16:29:10 PST)
- Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) (Fri Nov 18 2016 - 13:02:11 PST)
- Re: [AMBER] Restraints not working, What Am I doing Wrong? (Fri Nov 18 2016 - 10:26:46 PST)
- [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) (Fri Nov 18 2016 - 10:26:21 PST)
- [AMBER] Restraints not working, What Am I doing Wrong? (Mon Nov 14 2016 - 23:28:17 PST)
- [AMBER] How to visualize modes obtained from NMA (Wed Nov 02 2016 - 11:23:30 PDT)
Thomas Fox
- Re: [AMBER] Wierd line in amber-TI output Files (Fri Nov 25 2016 - 04:37:22 PST)
Tom Kurtzman
- Re: [AMBER] GIST: convergence of the translational entropy term (Fri Nov 11 2016 - 10:26:13 PST)
Tsibela German Tebello Mofokeng
- Re: [AMBER] creating parameters for integrins (Thu Nov 17 2016 - 23:40:38 PST)
- [AMBER] creating parameters for integrins (Thu Nov 17 2016 - 09:22:03 PST)
- Re: [AMBER] Help Constant pH MD calculations (Wed Nov 16 2016 - 01:06:46 PST)
- [AMBER] Help Constant pH MD calculations (Tue Nov 15 2016 - 08:32:45 PST)
Ulf Ryde
- Re: [AMBER] do_debugf changes energy (Fri Nov 04 2016 - 00:25:27 PDT)
- [AMBER] do_debugf changes energy (Thu Nov 03 2016 - 23:25:11 PDT)
Vlad Cojocaru
- Re: [AMBER] Umbrella simulation with an arbitrary bias potential (Mon Nov 07 2016 - 06:01:43 PST)
Vladislav Sláma
- Re: [AMBER] Problem with bonds in NAB (Thu Nov 24 2016 - 06:58:16 PST)
- Re: [AMBER] Problem with bonds in NAB (Tue Nov 08 2016 - 09:24:20 PST)
- [AMBER] Problem with bonds in NAB (Wed Nov 02 2016 - 08:39:12 PDT)
William Lees
- Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories (Thu Nov 10 2016 - 02:00:46 PST)
wjli
- [AMBER] Energy decomposition of free energy profiles (Tue Nov 15 2016 - 17:46:53 PST)
Xiangyu Jia
- [AMBER] virtual box in gas phase simulation (Fri Nov 04 2016 - 02:07:25 PDT)
- [AMBER] ntt = 6 and ibelly = 1 (Fri Nov 04 2016 - 01:50:03 PDT)
Yew Mun Yip
- [AMBER] How to create the .off/.lib file of the equilibrated non-aqueous solvent box? (Sat Nov 26 2016 - 22:05:12 PST)
Yigal Lahav
- [AMBER] micro iterations in QM/MM optimization. (Wed Nov 02 2016 - 07:28:57 PDT)
Yong Wang
- [AMBER] Problem to submit a pH-REMD on a GPU node (Fri Nov 25 2016 - 02:54:49 PST)
Zhe Li
- Re: [AMBER] Potential energy fluctuation of NVT ensemble (Sat Nov 05 2016 - 10:30:47 PDT)
- [AMBER] Potential energy fluctuation of NVT ensemble (Fri Nov 04 2016 - 15:15:49 PDT)
- [AMBER] Potential energy fluctuation of NVT ensemble (Thu Nov 03 2016 - 18:45:22 PDT)
zoran matovic
- Re: [AMBER] Ligand across membrane (Sun Nov 06 2016 - 23:38:25 PST)
东不拉
- [AMBER] mmpbsa error (Tue Nov 01 2016 - 01:31:34 PDT)
冯国强
- Re: [AMBER] AMBER Digest, Vol 1763, Issue 1 (Tue Nov 22 2016 - 00:52:41 PST)
- [AMBER] How to change the dielectric constant in the electrostatic energy term? (Sun Nov 20 2016 - 08:02:05 PST)
庄灿波
- [AMBER] MCPB.py and MMPBSA issue (Sat Nov 26 2016 - 01:32:53 PST)
杨满意
- [AMBER] How to generated correct inputfiles(.iprmtop and .inpcrd ) files (Tue Nov 22 2016 - 17:11:13 PST)
- [AMBER] generated correct inputfiles(.iprmtop and .inpcrd ) files (Fri Nov 18 2016 - 19:12:20 PST)
- [AMBER] Fw:problems for running step 2 of MCPB.py (Fri Nov 04 2016 - 00:00:56 PDT)

Amber Archive Nov 2016 by author