Amber Archive Dec 2017: by author

Abdul-Rashid III Sampaco
- Re: [AMBER] Problem in visualizing Amber16 trajecories in VMD (Tue Dec 05 2017 - 23:55:18 PST)
Andreas Tosstorff
- [AMBER] Meltcurve cpptraj (Fri Dec 22 2017 - 02:17:26 PST)
- [AMBER] cpptraj multiple trajectories (Mon Dec 18 2017 - 02:14:31 PST)
- [AMBER] error when running tleap from script, works fine from shell (Tue Dec 12 2017 - 05:52:58 PST)
- Re: [AMBER] cpptraj segmentation fault (Mon Dec 11 2017 - 08:07:21 PST)
- Re: [AMBER] cpptraj segmentation fault (Mon Dec 11 2017 - 07:47:12 PST)
- [AMBER] cpptraj segmentation fault (Mon Dec 11 2017 - 07:12:31 PST)
- Re: [AMBER] Amber Protonate for H++ (Thu Dec 07 2017 - 01:45:03 PST)
- Re: [AMBER] Amber Protonate for H++ (Thu Dec 07 2017 - 00:28:16 PST)
- [AMBER] Amber Protonate for H++ (Wed Dec 06 2017 - 09:58:19 PST)
Andrew Schaub
- Re: [AMBER] TI softcore single topology (HIE to HIP) - How do I generate a new lib file for an existing residue? (Thu Dec 14 2017 - 10:28:42 PST)
- Re: [AMBER] TI softcore single topology (HIE to HIP) - How do I generate a new lib file for an existing residue? (Thu Dec 14 2017 - 10:03:56 PST)
- [AMBER] TI softcore single topology (HIE to HIP) - How do I generate a new lib file for an existing residue? (Thu Dec 14 2017 - 09:58:50 PST)
- [AMBER] T.I. Sidechain setup (softcore potential) based off of A9 tutorial (Wed Dec 13 2017 - 11:17:58 PST)
anu chandra
- [AMBER] Queries about aMD simulation of metal-bound membrane protein and (Mon Dec 11 2017 - 01:59:43 PST)
Baker, Joseph
- Re: [AMBER] autoimage for a protein filament (Sat Dec 16 2017 - 15:56:43 PST)
- Re: [AMBER] autoimage for a protein filament (Wed Dec 13 2017 - 14:32:59 PST)
Batuhan Kav
- Re: [AMBER] Normalization of radial distribution function (Tue Dec 05 2017 - 01:40:54 PST)
Bill Ross
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Wed Dec 27 2017 - 00:44:40 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Tue Dec 26 2017 - 21:06:38 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Tue Dec 26 2017 - 16:14:03 PST)
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA (Tue Dec 26 2017 - 16:09:58 PST)
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA (Tue Dec 26 2017 - 16:01:20 PST)
- Re: [AMBER] Unable to compile mixed C/Fortran code. (Tue Dec 26 2017 - 04:18:48 PST)
- Re: [AMBER] box coordinates of the trajectory (Mon Dec 18 2017 - 20:47:51 PST)
- Re: [AMBER] Leap not running (Sat Dec 16 2017 - 04:13:02 PST)
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib (Fri Dec 15 2017 - 06:12:23 PST)
- Re: [AMBER] query regarding restraint_wt (Thu Dec 14 2017 - 02:24:56 PST)
- Re: [AMBER] query regarding restraint_wt (Thu Dec 14 2017 - 02:15:21 PST)
- Re: [AMBER] Solvating a molecule in amber (Mon Dec 11 2017 - 05:05:31 PST)
- Re: [AMBER] MCPB HEME (Mon Dec 11 2017 - 03:02:14 PST)
- Re: [AMBER] Solvating a molecule in amber (Sun Dec 10 2017 - 22:42:52 PST)
- Re: [AMBER] Solvating a molecule in amber (Sun Dec 10 2017 - 22:05:02 PST)
- Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions (Thu Dec 07 2017 - 02:39:20 PST)
- Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions (Thu Dec 07 2017 - 02:24:31 PST)
- Re: [AMBER] Problem in visualizing Amber16 trajecories in VMD (Tue Dec 05 2017 - 23:11:14 PST)
- Re: [AMBER] generation of topology and coordinate for glycan (Tue Dec 05 2017 - 22:32:03 PST)
- Re: [AMBER] generation of topology and coordinate for glycan (Tue Dec 05 2017 - 21:15:08 PST)
- Re: [AMBER] how to generate paramaters for GlcNH3 (Tue Dec 05 2017 - 14:29:28 PST)
Biplab Ghosh
- [AMBER] Problem in visualizing Amber16 trajecories in VMD (Tue Dec 05 2017 - 22:57:23 PST)
Carlos Simmerling
- Re: [AMBER] query regarding restraint_wt (Thu Dec 14 2017 - 03:51:48 PST)
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB (Tue Dec 12 2017 - 09:39:28 PST)
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB (Tue Dec 12 2017 - 05:23:38 PST)
- Re: [AMBER] Problem of loading complex (Fri Dec 08 2017 - 15:19:01 PST)
- Re: [AMBER] Problem of loading complex (Fri Dec 08 2017 - 12:51:33 PST)
- Re: [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti (Mon Dec 04 2017 - 11:32:22 PST)
Casalini Tommaso
- Re: [AMBER] MM-GBSA, acquire the value of each frame (Wed Dec 13 2017 - 08:00:26 PST)
Charles-Alexandre Mattelaer
- Re: [AMBER] CPPTRAJ HBOND (Fri Dec 29 2017 - 05:58:47 PST)
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA (Tue Dec 26 2017 - 08:29:27 PST)
Chase Zagorec-Marks
- [AMBER] End-of-File error occurring for Minimization run using Amoeba Force Field (Thu Dec 07 2017 - 09:48:28 PST)
Chitrak Gupta
- [AMBER] lipid 14 compatibility with FF14SB (Sat Dec 02 2017 - 11:17:33 PST)
Daniel Mermelstein
- Re: [AMBER] T.I. Sidechain setup (softcore potential) based off of A9 tutorial (Sun Dec 17 2017 - 14:49:24 PST)
- Re: [AMBER] To calculate TI using soft-core potential or not (Tue Dec 05 2017 - 13:54:40 PST)
Daniel Roe
- Re: [AMBER] CPPTRAJ HBOND (Fri Dec 29 2017 - 05:51:28 PST)
- Re: [AMBER] Meltcurve cpptraj (Fri Dec 22 2017 - 05:34:42 PST)
- Re: [AMBER] PCA.CPPTRAJ (Tue Dec 19 2017 - 06:23:37 PST)
- Re: [AMBER] CPPTRAJ hbond Analysis (Tue Dec 19 2017 - 06:23:10 PST)
- Re: [AMBER] box coordinates of the trajectory (Tue Dec 19 2017 - 06:19:43 PST)
- Re: [AMBER] PCA.CPPTRAJ (Mon Dec 18 2017 - 10:58:06 PST)
- Re: [AMBER] CPPTRAJ hbond Analysis (Mon Dec 18 2017 - 10:52:03 PST)
- Re: [AMBER] HREMD run (Mon Dec 18 2017 - 10:50:19 PST)
- Re: [AMBER] cpptraj multiple trajectories (Mon Dec 18 2017 - 10:48:15 PST)
- Re: [AMBER] PCA.CPPTRAJ (Fri Dec 15 2017 - 06:39:03 PST)
- Re: [AMBER] HREMD run (Fri Dec 15 2017 - 06:38:10 PST)
- Re: [AMBER] PCA.CPPTRAJ (Thu Dec 14 2017 - 10:21:41 PST)
- Re: [AMBER] autoimage for a protein filament (Thu Dec 14 2017 - 07:30:50 PST)
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB (Tue Dec 12 2017 - 05:52:05 PST)
- Re: [AMBER] cpptraj segmentation fault (Mon Dec 11 2017 - 08:39:22 PST)
- Re: [AMBER] cpptraj segmentation fault (Mon Dec 11 2017 - 08:38:35 PST)
- Re: [AMBER] cpptraj segmentation fault (Mon Dec 11 2017 - 07:53:48 PST)
- Re: [AMBER] cpptraj segmentation fault (Mon Dec 11 2017 - 07:41:10 PST)
- Re: [AMBER] imin=5 not working in AMBER16? (Fri Dec 01 2017 - 05:39:05 PST)
- Re: [AMBER] Problems with the "conbine" conmmand in LEaP (Fri Dec 01 2017 - 05:30:14 PST)
David A Case
- Re: [AMBER] NTWR,NTWX, NTPR increases for rest of simulation. (Wed Dec 27 2017 - 14:16:55 PST)
- Re: [AMBER] Which potential is used in TIP3P (How to calculate EPot by hand) (Wed Dec 27 2017 - 06:00:58 PST)
- Re: [AMBER] Unable to compile mixed C/Fortran code. (Tue Dec 26 2017 - 06:04:03 PST)
- Re: [AMBER] Function name not recognized in RdPar (Thu Dec 21 2017 - 05:13:14 PST)
- Re: [AMBER] error in distance restraints (Wed Dec 20 2017 - 18:53:56 PST)
- Re: [AMBER] Water-slab at constant pressure (Tue Dec 19 2017 - 05:21:58 PST)
- Re: [AMBER] Leap not running (Sat Dec 16 2017 - 05:20:35 PST)
- Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords (Fri Dec 15 2017 - 05:43:20 PST)
- Re: [AMBER] error when running tleap from script, works fine from shell (Wed Dec 13 2017 - 06:14:30 PST)
- Re: [AMBER] Problem of loading complex (Fri Dec 08 2017 - 17:51:32 PST)
- Re: [AMBER] Bonds between residues are broken (Fri Dec 08 2017 - 06:27:28 PST)
- Re: [AMBER] End-of-File error occurring for Minimization run using Amoeba Force Field (Fri Dec 08 2017 - 06:24:29 PST)
- Re: [AMBER] Amber Protonate for H++ (Fri Dec 08 2017 - 06:14:58 PST)
- Re: [AMBER] Amber Protonate for H++ (Wed Dec 06 2017 - 11:14:48 PST)
- Re: [AMBER] Problem in visualizing Amber16 trajecories in VMD (Wed Dec 06 2017 - 05:08:36 PST)
- Re: [AMBER] lipid 14 compatibility with FF14SB (Sun Dec 03 2017 - 05:39:45 PST)
- Re: [AMBER] imin=5 not working in AMBER16? (Fri Dec 01 2017 - 09:40:52 PST)
David Cerutti
- Re: [AMBER] Which potential is used in TIP3P (How to calculate EPot by hand) (Wed Dec 27 2017 - 05:34:42 PST)
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA (Tue Dec 26 2017 - 12:11:26 PST)
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA (Tue Dec 26 2017 - 09:54:02 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Tue Dec 26 2017 - 06:12:01 PST)
- Re: [AMBER] Does pmemd.cuda support QM/MM (Tue Dec 12 2017 - 05:01:19 PST)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Fri Dec 08 2017 - 12:18:39 PST)
Dolivier
- Re: [AMBER] MM-GBSA, acquire the value of each frame (Wed Dec 13 2017 - 08:00:47 PST)
Dow Hurst
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Fri Dec 08 2017 - 11:34:47 PST)
Dr. Anselm Horn
- [AMBER] [MGMS-DS]: Molecular Modelling Workshop March 12-14, 2018 in Erlangen, Germany (Tue Dec 19 2017 - 01:36:28 PST)
Dr. MANAS MONDAL
- Re: [AMBER] HREMD run (Mon Dec 18 2017 - 18:32:45 PST)
- Re: [AMBER] HREMD run (Mon Dec 18 2017 - 03:28:23 PST)
- [AMBER] HREMD run (Thu Dec 14 2017 - 17:47:56 PST)
Elvis Martis
- Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords (Fri Dec 15 2017 - 06:07:14 PST)
- Re: [AMBER] Does pmemd.cuda support QM/MM (Tue Dec 12 2017 - 05:03:18 PST)
- Re: [AMBER] Does pmemd.cuda support QM/MM (Fri Dec 08 2017 - 02:27:12 PST)
Gao Zhenting
- Re: [AMBER] A small but fatal Typo in "LEaP Tutorial" (Tue Dec 26 2017 - 18:16:48 PST)
- [AMBER] Fwd: A small but fatal Typo in "LEaP Tutorial" (Tue Dec 26 2017 - 01:01:24 PST)
George M. Giambasu
- Re: [AMBER] Normalization of radial distribution function (Mon Dec 04 2017 - 07:28:33 PST)
Giovanni Grazioso
- [AMBER] MM-GBSA, acquire the value of each frame (Wed Dec 13 2017 - 07:56:30 PST)
Goetz, Andreas
- Re: [AMBER] Several questions about Amber adaptive QM/MM MD. (Fri Dec 22 2017 - 17:45:39 PST)
Gustavo Seabra
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! (Fri Dec 01 2017 - 03:23:40 PST)
Hadházi Ádám
- [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti (Mon Dec 04 2017 - 10:41:10 PST)
Hai Nguyen
- Re: [AMBER] parmed error (Thu Dec 21 2017 - 18:53:52 PST)
- Re: [AMBER] HREMD run (Mon Dec 18 2017 - 18:40:45 PST)
- Re: [AMBER] CPPTRAJ hbond Analysis (Mon Dec 18 2017 - 02:47:52 PST)
- Re: [AMBER] Error with installation, amber 17 on centos server (Tue Dec 12 2017 - 09:22:14 PST)
Investigador Química
- Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords (Tue Dec 19 2017 - 03:27:19 PST)
- [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords (Thu Dec 14 2017 - 16:42:23 PST)
Jan Ludwiczak
- [AMBER] Phosphohistidine residues (Thu Dec 28 2017 - 08:34:50 PST)
Jason Swails
- Re: [AMBER] Error: No module named parmed.scripts (Sun Dec 03 2017 - 20:43:17 PST)
jesus berlanga
- [AMBER] Water-slab at constant pressure (Mon Dec 18 2017 - 18:38:52 PST)
Johannes Kalliauer
- [AMBER] Which potential is used in TIP3P (How to calculate EPot by hand) (Wed Dec 27 2017 - 05:00:32 PST)
Junmei Wang
- Re: [AMBER] Modified amino acid (Thu Dec 07 2017 - 07:49:49 PST)
- Re: [AMBER] antechamber: prepgen mainchain file character limit (Fri Dec 01 2017 - 11:35:35 PST)
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! (Fri Dec 01 2017 - 11:30:46 PST)
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! (Fri Dec 01 2017 - 09:29:41 PST)
junmwang.gmail.com
- Re: [AMBER] Modified amino acid (Thu Dec 07 2017 - 04:29:44 PST)
Lachele Foley
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Thu Dec 28 2017 - 22:30:44 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Wed Dec 27 2017 - 22:46:35 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Wed Dec 27 2017 - 00:55:41 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Wed Dec 27 2017 - 00:36:04 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Tue Dec 26 2017 - 20:42:38 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Tue Dec 26 2017 - 20:22:42 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Tue Dec 26 2017 - 19:51:32 PST)
- Re: [AMBER] how to generate paramaters for GlcNH3 (Fri Dec 08 2017 - 15:01:39 PST)
- Re: [AMBER] pdf of O-GlcNAc Ser and Thr (Thu Dec 07 2017 - 19:11:34 PST)
- Re: [AMBER] generation of topology and coordinate for glycan (Thu Dec 07 2017 - 19:09:31 PST)
Leena Aggarwal
- [AMBER] box coordinates of the trajectory (Mon Dec 18 2017 - 20:44:32 PST)
- Re: [AMBER] query regarding restraint_wt (Thu Dec 14 2017 - 02:18:42 PST)
- [AMBER] query regarding restraint_wt (Thu Dec 14 2017 - 01:57:34 PST)
Li, Xinghui
- [AMBER] pdf of O-GlcNAc Ser and Thr (Thu Dec 07 2017 - 11:15:07 PST)
Lorenzo Gontrani
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ (Mon Dec 04 2017 - 22:17:54 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ (Sun Dec 03 2017 - 03:10:43 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ (Sun Dec 03 2017 - 02:51:17 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ (Sun Dec 03 2017 - 02:49:49 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ (Sun Dec 03 2017 - 02:19:42 PST)
Marcos Serrou do Amaral
- Re: [AMBER] MCPB HEME (Mon Dec 11 2017 - 05:53:14 PST)
Michael Shokhen
- [AMBER] error in distance restraints (Wed Dec 20 2017 - 13:40:03 PST)
Mingyuan_xu
- [AMBER] Several questions about Amber adaptive QM/MM MD. (Mon Dec 18 2017 - 08:39:00 PST)
MinYuan
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib (Fri Dec 15 2017 - 06:04:19 PST)
- [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib (Tue Dec 12 2017 - 19:11:20 PST)
- [AMBER] MCPB.py deal with two metal-like sites simultaneously (Tue Dec 12 2017 - 02:14:52 PST)
- Re: [AMBER] Does pmemd.cuda support QM/MM (Sat Dec 09 2017 - 04:15:03 PST)
- [AMBER] Does pmemd.cuda support QM/MM (Fri Dec 08 2017 - 00:03:47 PST)
- Re: [AMBER] Problem with running Example2 from MCPB.py reference SI file (Tue Dec 05 2017 - 03:33:18 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ (Tue Dec 05 2017 - 03:31:48 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ (Mon Dec 04 2017 - 18:12:48 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ (Mon Dec 04 2017 - 18:09:03 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ (Sun Dec 03 2017 - 03:57:24 PST)
- [AMBER] MCPB.py to generate force field parameter for metal ion As3+ (Sat Dec 02 2017 - 19:49:17 PST)
- [AMBER] Problem with running Example2 from MCPB.py reference SI file (Sat Dec 02 2017 - 19:25:29 PST)
minyuan.mail.ustc.edu.cn
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib (Sun Dec 17 2017 - 22:49:02 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ (Sun Dec 03 2017 - 02:56:59 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ (Sun Dec 03 2017 - 02:33:18 PST)
mirzo
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! (Fri Dec 01 2017 - 11:43:57 PST)
mish
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Thu Dec 28 2017 - 00:49:43 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Wed Dec 27 2017 - 04:23:05 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Tue Dec 26 2017 - 21:09:11 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Tue Dec 26 2017 - 20:56:13 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Tue Dec 26 2017 - 20:36:44 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Tue Dec 26 2017 - 20:10:40 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Tue Dec 26 2017 - 16:27:32 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Tue Dec 26 2017 - 16:12:02 PST)
- [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? (Tue Dec 26 2017 - 00:09:35 PST)
Morrow,John Kenneth
- [AMBER] Binding energy of ligand with homology model (Thu Dec 21 2017 - 11:45:31 PST)
Mustafa Alhaji Isa
- Re: [AMBER] Problem of loading complex (Fri Dec 08 2017 - 13:08:31 PST)
- [AMBER] Problem of loading complex (Fri Dec 08 2017 - 12:48:55 PST)
Myron
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB (Tue Dec 12 2017 - 08:15:48 PST)
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB (Tue Dec 12 2017 - 08:07:10 PST)
- [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB (Tue Dec 12 2017 - 04:26:16 PST)
Naina Singh
- [AMBER] Leap not running (Sat Dec 16 2017 - 04:10:18 PST)
Nikolay N. Kuzmich
- [AMBER] Atom restraints in AMBER (Fri Dec 22 2017 - 00:29:09 PST)
p.kartheek
- Re: [AMBER] parmed error (Thu Dec 21 2017 - 11:26:16 PST)
Paul Mortenson
- Re: [AMBER] imin=5 not working in AMBER16? (Mon Dec 04 2017 - 06:04:04 PST)
- Re: [AMBER] imin=5 not working in AMBER16? (Fri Dec 01 2017 - 07:08:44 PST)
- Re: [AMBER] imin=5 not working in AMBER16? (Thu Nov 30 2017 - 23:52:26 PST)
Pengfei Li
- Re: [AMBER] A small but fatal Typo in "LEaP Tutorial" (Tue Dec 26 2017 - 09:49:18 PST)
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib (Wed Dec 20 2017 - 14:57:29 PST)
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib (Fri Dec 15 2017 - 07:58:53 PST)
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib (Wed Dec 13 2017 - 08:54:52 PST)
- Re: [AMBER] MCPB.py deal with two metal-like sites simultaneously (Wed Dec 13 2017 - 08:54:11 PST)
- Re: [AMBER] MCPB.py how to insert the heteroatom heme in the one domain of macromolecule (Mon Dec 04 2017 - 14:22:19 PST)
- Re: [AMBER] Problem with running Example2 from MCPB.py reference SI file (Mon Dec 04 2017 - 14:12:11 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ (Mon Dec 04 2017 - 14:07:12 PST)
Praneeth Bommisetti
- [AMBER] Fwd: Re: Error with installation, amber 17 on centos server (Tue Dec 12 2017 - 10:05:54 PST)
- [AMBER] Error with installation, amber 17 on centos server (Tue Dec 12 2017 - 09:16:03 PST)
Rajarshi Roy
- Re: [AMBER] Modified amino acid (Fri Dec 08 2017 - 02:24:06 PST)
- Re: [AMBER] Modified amino acid (Thu Dec 07 2017 - 05:25:20 PST)
- [AMBER] Modified amino acid (Thu Dec 07 2017 - 03:37:22 PST)
- Re: [AMBER] generation of topology and coordinate for glycan (Tue Dec 05 2017 - 22:14:02 PST)
- [AMBER] generation of topology and coordinate for glycan (Tue Dec 05 2017 - 20:56:41 PST)
Rana Rehan Khalid
- Re: [AMBER] DSSP CPPtraj (Sun Dec 31 2017 - 07:05:20 PST)
- [AMBER] DSSP CPPtraj (Sun Dec 31 2017 - 06:27:35 PST)
- Re: [AMBER] CPPTRAJ HBOND (Fri Dec 29 2017 - 08:26:26 PST)
- [AMBER] CPPTRAJ HBOND (Fri Dec 29 2017 - 05:40:31 PST)
- Re: [AMBER] NTWR,NTWX, NTPR increases for rest of simulation. (Wed Dec 27 2017 - 14:19:44 PST)
- [AMBER] NTWR,NTWX, NTPR increases for rest of simulation. (Wed Dec 27 2017 - 12:47:14 PST)
- Re: [AMBER] hbond occupancy plot cpptraj (Sun Dec 24 2017 - 04:45:38 PST)
- [AMBER] hbond occupancy plot cpptraj (Sat Dec 23 2017 - 17:38:35 PST)
- Re: [AMBER] PCA.CPPTRAJ (Thu Dec 21 2017 - 04:36:13 PST)
- Re: [AMBER] CPPTRAJ hbond Analysis (Wed Dec 20 2017 - 08:05:26 PST)
- Re: [AMBER] PCA.CPPTRAJ (Tue Dec 19 2017 - 06:24:51 PST)
- Re: [AMBER] CPPTRAJ hbond Analysis (Mon Dec 18 2017 - 14:36:49 PST)
- Re: [AMBER] PCA.CPPTRAJ (Mon Dec 18 2017 - 13:43:33 PST)
- Re: [AMBER] PCA.CPPTRAJ (Mon Dec 18 2017 - 13:16:27 PST)
- Re: [AMBER] CPPTRAJ hbond Analysis (Mon Dec 18 2017 - 03:04:23 PST)
- [AMBER] CPPTRAJ hbond Analysis (Sun Dec 17 2017 - 13:17:13 PST)
- Re: [AMBER] PCA.CPPTRAJ (Sat Dec 16 2017 - 07:25:38 PST)
- Re: [AMBER] PCA.CPPTRAJ (Sat Dec 16 2017 - 05:38:13 PST)
- Re: [AMBER] PCA.CPPTRAJ (Sat Dec 16 2017 - 00:05:12 PST)
- Re: [AMBER] PCA.CPPTRAJ (Thu Dec 14 2017 - 13:03:41 PST)
- [AMBER] PCA.CPPTRAJ (Wed Dec 13 2017 - 13:58:26 PST)
- Re: [AMBER] MCPB HEME (Mon Dec 11 2017 - 06:33:52 PST)
- [AMBER] MCPB HEME (Mon Dec 11 2017 - 03:00:11 PST)
- [AMBER] helix broken during minimization step (Mon Dec 04 2017 - 06:52:34 PST)
- [AMBER] Residue Protonation State (Sat Dec 02 2017 - 01:07:50 PST)
Rinsha Chk
- Re: [AMBER] Function name not recognized in RdPar (Thu Dec 21 2017 - 05:21:45 PST)
- Re: [AMBER] Function name not recognized in RdPar (Thu Dec 21 2017 - 05:20:48 PST)
- [AMBER] Function name not recognized in RdPar (Thu Dec 21 2017 - 00:24:53 PST)
Rivera, Miguel
- Re: [AMBER] Does pmemd.cuda support QM/MM (Tue Dec 12 2017 - 04:20:32 PST)
Robert Molt
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA (Tue Dec 26 2017 - 17:24:57 PST)
Ross Walker
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA (Tue Dec 26 2017 - 15:43:22 PST)
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA (Tue Dec 26 2017 - 11:57:10 PST)
- [AMBER] Troubling changes to NVIDIA Driver EULA (Tue Dec 26 2017 - 08:07:25 PST)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Sat Dec 09 2017 - 09:53:31 PST)
- Re: [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti (Mon Dec 04 2017 - 11:38:14 PST)
- Re: [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti (Mon Dec 04 2017 - 10:48:15 PST)
Sanaa ALAbbad
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! (Fri Dec 01 2017 - 15:54:41 PST)
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! (Fri Dec 01 2017 - 11:13:57 PST)
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! (Fri Dec 01 2017 - 09:41:17 PST)
Schmid, Ralf (Dr.)
- Re: [AMBER] Residue Protonation State (Sat Dec 02 2017 - 09:08:40 PST)
Scott Le Grand
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Sat Dec 09 2017 - 11:35:18 PST)
Sergey Samsonov
- [AMBER] MMPBSA.py and S-S bonds between different chains (Tue Dec 12 2017 - 07:58:59 PST)
Setyanto Md
- Re: [AMBER] Amber Protonate for H++ (Thu Dec 07 2017 - 05:30:43 PST)
- Re: [AMBER] Amber Protonate for H++ (Wed Dec 06 2017 - 19:17:44 PST)
- Re: [AMBER] Error: No module named parmed.scripts (Mon Dec 04 2017 - 06:50:00 PST)
- [AMBER] Error: No module named parmed.scripts (Thu Nov 30 2017 - 15:12:49 PST)
Shilpa Gupta
- [AMBER] Parmed topology file have ifbox=0 (Wed Dec 13 2017 - 00:36:57 PST)
- Re: [AMBER] Solvating a molecule in amber (Mon Dec 11 2017 - 05:17:58 PST)
- Re: [AMBER] Solvating a molecule in amber (Mon Dec 11 2017 - 04:20:48 PST)
- Re: [AMBER] Solvating a molecule in amber (Sun Dec 10 2017 - 22:09:28 PST)
- [AMBER] Solvating a molecule in amber (Sun Dec 10 2017 - 20:37:41 PST)
- Re: [AMBER] Bonds between residues are broken (Fri Dec 08 2017 - 08:22:18 PST)
- [AMBER] Bonds between residues are broken (Thu Dec 07 2017 - 21:33:59 PST)
suma jayakrishnan
- [AMBER] Unable to compile mixed C/Fortran code. (Tue Dec 26 2017 - 03:53:18 PST)
Szymon Żaczek
- Re: [AMBER] Normalization of radial distribution function (Tue Dec 05 2017 - 03:31:08 PST)
- Re: [AMBER] Normalization of radial distribution function (Tue Dec 05 2017 - 00:09:38 PST)
- [AMBER] Normalization of radial distribution function (Sun Dec 03 2017 - 10:38:08 PST)
Tarsis
- Re: [AMBER] how to generate paramaters for GlcNH3 (Thu Dec 07 2017 - 11:37:09 PST)
- [AMBER] how to generate paramaters for GlcNH3 (Tue Dec 05 2017 - 14:19:25 PST)
Tarsis Ferreira
- Re: [AMBER] how to generate paramaters for GlcNH3 (Fri Dec 08 2017 - 09:34:17 PST)
Thakur, Abhishek
- [AMBER] parmed error (Thu Dec 21 2017 - 10:44:56 PST)
- [AMBER] more than 100% hydrogen bond population (Wed Dec 20 2017 - 12:38:59 PST)
Tru Huynh
- Re: [AMBER] Error with installation, amber 17 on centos server (Tue Dec 12 2017 - 10:23:34 PST)
Vaibhav Dixit
- [AMBER] implicit models for other solvents and non-standard solvents (Fri Dec 01 2017 - 04:35:11 PST)
Vlad Cojocaru
- Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions (Thu Dec 07 2017 - 02:52:10 PST)
- Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions (Thu Dec 07 2017 - 02:35:58 PST)
- [AMBER] force addions to avoid replacing specific solvent molecules by ions (Thu Dec 07 2017 - 02:14:41 PST)
Yang Jinpeng
- [AMBER] The paramters of frcmod.chcl3 (Wed Dec 06 2017 - 19:25:50 PST)
- [AMBER] To calculate TI using soft-core potential or not (Tue Dec 05 2017 - 00:35:09 PST)
Yin, Guowei
- [AMBER] pdf of O-GlcNAc Ser and Thr (Thu Dec 07 2017 - 09:42:50 PST)
- [AMBER] pdf of O-GlcNAc Ser and Thr (Thu Dec 07 2017 - 07:57:35 PST)
杨满意
- Re: [AMBER] Problems with the "conbine" conmmand in LEaP (Fri Dec 01 2017 - 17:23:16 PST)
- [AMBER] Problems with the "conbine" conmmand in LEaP (Thu Nov 30 2017 - 16:56:33 PST)

Amber Archive Dec 2017 by author