Amber Archive Oct 2017: by author

Adrian Roitberg
- Re: [AMBER] disulfide bonds braking during MD simulation (Wed Oct 25 2017 - 13:31:58 PDT)
- Re: [AMBER] error with restraint distance minimization (Wed Oct 25 2017 - 09:08:57 PDT)
- Re: [AMBER] Bias Towards the Periodic Boundary (Wed Oct 18 2017 - 11:22:01 PDT)
- Re: [AMBER] Running Explicit pH MD (Mon Oct 16 2017 - 08:31:03 PDT)
- Re: [AMBER] Ruthenium complex MD simulation ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported! (Mon Oct 09 2017 - 16:48:50 PDT)
Alain Chaumont
- [AMBER] pmemd.cuda and rigid CH2Cl2 (Tue Oct 10 2017 - 04:31:12 PDT)
Albert
- Re: [AMBER] how to generated data for plot? (Wed Oct 25 2017 - 11:50:18 PDT)
- [AMBER] how to generated data for plot? (Fri Oct 20 2017 - 04:17:17 PDT)
- Re: [AMBER] REMD job failed (Tue Oct 10 2017 - 07:44:56 PDT)
- [AMBER] REMD job failed (Tue Oct 10 2017 - 07:34:32 PDT)
- Re: [AMBER] about Paramfit (Fri Oct 06 2017 - 23:59:56 PDT)
- [AMBER] about Paramfit (Fri Oct 06 2017 - 14:03:21 PDT)
Alessandro Contini
- Re: [AMBER] MM/PBSA or MM/GBSA (Wed Oct 25 2017 - 00:03:03 PDT)
- Re: [AMBER] MM/PBSA or MM/GBSA (Tue Oct 24 2017 - 08:06:50 PDT)
Alessandro Mariani
- Re: [AMBER] Amber16 electric field parameters (Mon Oct 02 2017 - 01:18:57 PDT)
Alonso Martinez, Diego
- [AMBER] Binding affinity of different small molecules to a complex of metal + protein + DNA (Fri Oct 27 2017 - 06:17:57 PDT)
Amani Eshtiwi
- Re: [AMBER] System preparation for protein with Multiple Zn-CCCC (Fri Oct 06 2017 - 19:59:06 PDT)
Amy Rice
- Re: [AMBER] Cpptraj HBond salt bridge output question (Wed Oct 25 2017 - 08:57:15 PDT)
- [AMBER] Cpptraj HBond salt bridge output question (Wed Oct 25 2017 - 08:22:27 PDT)
Andreas Tosstorff
- Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 (Sat Oct 28 2017 - 13:47:33 PDT)
- Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 (Sat Oct 28 2017 - 02:24:57 PDT)
- [AMBER] Wrong connectivity after antechamber/Gaussian16 (Fri Oct 27 2017 - 11:19:04 PDT)
- [AMBER] WHAM, DHAM, MBAR, BAR, TI... (Thu Oct 19 2017 - 09:04:22 PDT)
- Re: [AMBER] Restarting REMD (Fri Oct 13 2017 - 03:43:02 PDT)
- Re: [AMBER] Restarting REMD (Fri Oct 13 2017 - 01:17:37 PDT)
- [AMBER] Restarting REMD (Fri Oct 13 2017 - 01:13:54 PDT)
Andrew Schaub
- Re: [AMBER] RESP charges for a peptide-bound probe with R.E.D. (Mon Oct 16 2017 - 17:15:44 PDT)
- Re: [AMBER] help for the installation of Ambertools 17 on Mac (Mon Oct 16 2017 - 14:42:49 PDT)
- Re: [AMBER] vague error when running constant ph simulations (Wed Oct 11 2017 - 13:06:45 PDT)
- Re: [AMBER] vague error when running constant ph simulations (Wed Oct 11 2017 - 12:24:13 PDT)
- [AMBER] vague error when running constant ph simulations (Tue Oct 03 2017 - 21:08:01 PDT)
Anton Perera
- [AMBER] Error in preparation of Zn.lib (Fri Oct 06 2017 - 01:12:44 PDT)
Arthi Venkat
- Re: [AMBER] Forecefield error (Tue Oct 24 2017 - 20:30:39 PDT)
- Re: [AMBER] Forecefield error (Tue Oct 24 2017 - 20:16:41 PDT)
- [AMBER] Forecefield error (Tue Oct 24 2017 - 20:05:28 PDT)
Arun Srikanth
- [AMBER] About paramfit 1-4 scaling (Tue Oct 24 2017 - 17:47:18 PDT)
- Re: [AMBER] About penalty scores (Tue Oct 24 2017 - 07:29:15 PDT)
- [AMBER] About penalty scores (Mon Oct 23 2017 - 17:02:08 PDT)
ATUL KUMAR
- Re: [AMBER] making 6M GDMCl box (Thu Oct 12 2017 - 03:34:07 PDT)
- [AMBER] making 6M GDMCl box (Thu Oct 12 2017 - 02:58:08 PDT)
- [AMBER] Hydrogen Bond (Mon Oct 09 2017 - 05:48:23 PDT)
- [AMBER] Hydrogen Bond (Mon Oct 09 2017 - 04:54:07 PDT)
Batuhan Kav
- Re: [AMBER] DPPG lipid bilayer simulation using Lipid17 - too small area per lipid ? (Wed Oct 04 2017 - 11:41:43 PDT)
Bill Ross
- Re: [AMBER] Constant temperature is not constant from the beginning (Mon Oct 30 2017 - 22:16:08 PDT)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Mon Oct 30 2017 - 14:57:33 PDT)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Mon Oct 30 2017 - 14:10:45 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation (Wed Oct 25 2017 - 13:33:06 PDT)
- Re: [AMBER] Can we use OPLS force field in AMBER (Wed Oct 25 2017 - 00:11:27 PDT)
- Re: [AMBER] Can we use OPLS force field in AMBER (Tue Oct 24 2017 - 07:01:47 PDT)
- Re: [AMBER] effect of MPI problem on MD calculations (Fri Oct 20 2017 - 10:05:29 PDT)
- Re: [AMBER] how we can visualized the bonds after saving on of the MD frame into pdb file. (Thu Oct 19 2017 - 12:06:43 PDT)
- Re: [AMBER] Protein drift from solvent box (Thu Oct 19 2017 - 07:29:39 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 23:25:21 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 23:18:32 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 23:11:06 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 23:09:37 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 22:48:17 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 22:38:23 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 22:29:02 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 22:12:03 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 21:41:18 PDT)
- Re: [AMBER] Specify amount of memory (Sun Oct 15 2017 - 01:39:11 PDT)
- Re: [AMBER] How to show double bond connection between N=O2 (Sat Oct 14 2017 - 15:47:40 PDT)
- Re: [AMBER] Converting atom names from NAMD to AMBER (Fri Oct 13 2017 - 13:36:55 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Thu Oct 12 2017 - 22:52:13 PDT)
- Re: [AMBER] Error reading Ruthenium complex residue (Thu Oct 12 2017 - 14:57:24 PDT)
- Re: [AMBER] making 6M GDMCl box (Thu Oct 12 2017 - 12:06:25 PDT)
- Re: [AMBER] making 6M GDMCl box (Thu Oct 12 2017 - 03:02:03 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Thu Oct 12 2017 - 02:11:08 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Wed Oct 11 2017 - 21:27:32 PDT)
- Re: [AMBER] output file .out file deleted mistakenly (Wed Oct 11 2017 - 11:15:25 PDT)
- Re: [AMBER] output file .out file deleted mistakenly (Wed Oct 11 2017 - 11:06:30 PDT)
- Re: [AMBER] output file .out file deleted mistakenly (Wed Oct 11 2017 - 11:04:25 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Wed Oct 11 2017 - 10:31:45 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Wed Oct 11 2017 - 00:05:25 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Tue Oct 10 2017 - 23:05:47 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Tue Oct 10 2017 - 08:05:03 PDT)
- Re: [AMBER] System preparation for protein with Multiple Zn-CCCC (Sat Oct 07 2017 - 16:37:08 PDT)
- Re: [AMBER] AmberTools17 and shape.h (Thu Oct 05 2017 - 16:53:21 PDT)
- Re: [AMBER] AmberTools17 and shape.h (Thu Oct 05 2017 - 16:51:02 PDT)
- Re: [AMBER] net charge problem of Amber Lipid14 Force Field (Thu Oct 05 2017 - 16:08:48 PDT)
- Re: [AMBER] net charge problem of Amber Lipid14 Force Field (Thu Oct 05 2017 - 15:56:08 PDT)
Carlos Simmerling
- Re: [AMBER] restraint_wt applied to wrong atoms (Mon Oct 30 2017 - 05:22:20 PDT)
- Re: [AMBER] Use of pmemd for minimisation and equilibration (Fri Oct 27 2017 - 09:06:47 PDT)
- Re: [AMBER] STOP PMEMD Terminated Abnormally! (Thu Oct 26 2017 - 05:23:44 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation (Wed Oct 25 2017 - 13:56:03 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation (Wed Oct 25 2017 - 12:59:28 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation (Wed Oct 25 2017 - 11:44:55 PDT)
- Re: [AMBER] Forecefield error (Wed Oct 25 2017 - 03:40:25 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation (Tue Oct 24 2017 - 08:07:21 PDT)
- Re: [AMBER] MM/PBSA or MM/GBSA (Tue Oct 24 2017 - 06:51:48 PDT)
- Re: [AMBER] Independent production runs (Fri Oct 20 2017 - 05:08:22 PDT)
- Re: [AMBER] how we can visualized the bonds after saving on of the MD frame into pdb file. (Thu Oct 19 2017 - 11:19:00 PDT)
- Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? (Thu Oct 19 2017 - 06:46:13 PDT)
- Re: [AMBER] Restarting REMD (Fri Oct 13 2017 - 03:34:15 PDT)
- Re: [AMBER] Ruthenium complex MD simulation ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported! (Mon Oct 09 2017 - 16:54:47 PDT)
- Re: [AMBER] Current rmsd from reference in targeted MD (Wed Oct 04 2017 - 06:04:55 PDT)
- Re: [AMBER] Current rmsd from reference in targeted MD (Wed Oct 04 2017 - 05:38:13 PDT)
- Re: [AMBER] Current rmsd from reference in targeted MD (Wed Oct 04 2017 - 03:30:59 PDT)
- Re: [AMBER] Current rmsd from reference in targeted MD (Tue Oct 03 2017 - 09:44:00 PDT)
Charles Mariasoosai
- [AMBER] Is it possible to simulate Indium (coupled with sulpher and copper) nano material in amber? (Tue Oct 03 2017 - 09:33:25 PDT)
Chris Moth
- Re: [AMBER] AMBER (Thu Oct 05 2017 - 05:16:11 PDT)
Chris Neale
- Re: [AMBER] Independent MD runs (Wed Oct 04 2017 - 22:30:01 PDT)
Christopher Benjamin Coffey
- Re: [AMBER] AmberTools17 and shape.h (Fri Oct 06 2017 - 11:01:03 PDT)
- Re: [AMBER] AmberTools17 and shape.h (Thu Oct 05 2017 - 16:26:09 PDT)
- [AMBER] AmberTools17 and shape.h (Thu Oct 05 2017 - 07:11:55 PDT)
Chunli Yan
- Re: [AMBER] How to put anchor_position for RMSD collective variable Value in string methods (Fri Oct 13 2017 - 09:37:00 PDT)
- [AMBER] How to put anchor_position for RMSD collective variable Value in string methods (Mon Oct 09 2017 - 05:45:01 PDT)
- Re: [AMBER] colvar in string methods (Wed Oct 04 2017 - 20:51:16 PDT)
- [AMBER] colvar in string methods (Wed Oct 04 2017 - 19:57:27 PDT)
colvin
- [AMBER] Independent MD runs (Wed Oct 04 2017 - 20:11:19 PDT)
Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Running Explicit pH MD (Mon Oct 30 2017 - 08:24:00 PDT)
- Re: [AMBER] Running Explicit pH MD (Mon Oct 30 2017 - 08:14:03 PDT)
- Re: [AMBER] frozen atoms. (Fri Oct 27 2017 - 12:30:14 PDT)
- Re: [AMBER] frozen atoms. (Fri Oct 27 2017 - 09:28:32 PDT)
- Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? (Thu Oct 19 2017 - 07:28:38 PDT)
- Re: [AMBER] Restarting pH-REMD simulations after abnormal termination (Fri Oct 13 2017 - 07:07:18 PDT)
- Re: [AMBER] REMD job failed (Tue Oct 10 2017 - 07:41:03 PDT)
Crystal Vander Zanden
- [AMBER] Test failed after installing Amber Tools 17 (Tue Oct 31 2017 - 13:18:24 PDT)
Daniel Mermelstein
- Re: [AMBER] Thermodynamic integration/switch off/on cloumbic and vdw interactions (Mon Oct 09 2017 - 10:40:02 PDT)
Daniel Roe
- Re: [AMBER] pdb4amber bug - incorrect "CONECT" between chains (Tue Oct 31 2017 - 06:07:05 PDT)
- Re: [AMBER] Cpptraj HBond salt bridge output question (Wed Oct 25 2017 - 08:39:56 PDT)
- Re: [AMBER] Protein drift from solvent box (Fri Oct 20 2017 - 11:43:08 PDT)
- Re: [AMBER] how to generated data for plot? (Fri Oct 20 2017 - 06:39:31 PDT)
- Re: [AMBER] trajout format with cpptraj in Ambertools 17 (Tue Oct 17 2017 - 08:52:07 PDT)
- Re: [AMBER] Vector command in cpptraj (Mon Oct 16 2017 - 06:23:37 PDT)
- Re: [AMBER] Converting atom names from NAMD to AMBER (Fri Oct 13 2017 - 10:32:16 PDT)
- Re: [AMBER] parmstrip with cpptraj in Ambertools 17 (Fri Oct 13 2017 - 09:54:59 PDT)
- Re: [AMBER] parmstrip with cpptraj in Ambertools 17 (Fri Oct 13 2017 - 07:25:43 PDT)
- Re: [AMBER] parmstrip with cpptraj in Ambertools 17 (Thu Oct 12 2017 - 17:35:39 PDT)
- Re: [AMBER] output file .out file deleted mistakenly (Thu Oct 12 2017 - 06:02:55 PDT)
- Re: [AMBER] Hydrogen Bond (Tue Oct 10 2017 - 12:16:35 PDT)
- Re: [AMBER] REMD job failed (Tue Oct 10 2017 - 10:15:37 PDT)
- Re: [AMBER] Vector math: a couple of questions (Wed Oct 04 2017 - 09:54:11 PDT)
- Re: [AMBER] Vector math: a couple of questions (Wed Oct 04 2017 - 09:30:02 PDT)
- Re: [AMBER] How to save reimaged trajectory file during MD? (Mon Oct 02 2017 - 06:05:16 PDT)
- Re: [AMBER] identiy the step of interaction from an entire trajectory (Mon Oct 02 2017 - 05:55:48 PDT)
- Re: [AMBER] trajout last x frames cpptraj (Mon Oct 02 2017 - 05:31:23 PDT)
danilo gonzalez
- Re: [AMBER] frozen atoms. (Fri Oct 27 2017 - 11:40:25 PDT)
- [AMBER] frozen atoms. (Fri Oct 27 2017 - 09:14:30 PDT)
David A Case
- Re: [AMBER] Test failed after installing Amber Tools 17 (Tue Oct 31 2017 - 17:36:14 PDT)
- Re: [AMBER] pdb4amber bug - incorrect "CONECT" between chains (Tue Oct 31 2017 - 05:12:23 PDT)
- Re: [AMBER] warning Close contact (Mon Oct 30 2017 - 05:02:26 PDT)
- Re: [AMBER] Error in calculating MM-PBSA (Sun Oct 29 2017 - 05:14:01 PDT)
- Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 (Sat Oct 28 2017 - 17:31:21 PDT)
- Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 (Sat Oct 28 2017 - 05:16:25 PDT)
- Re: [AMBER] frozen atoms. (Fri Oct 27 2017 - 12:23:44 PDT)
- Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 (Fri Oct 27 2017 - 12:20:59 PDT)
- Re: [AMBER] Error Due to Duplicate residues atoms (Fri Oct 27 2017 - 12:15:49 PDT)
- Re: [AMBER] Use of pmemd for minimisation and equilibration (Fri Oct 27 2017 - 09:01:35 PDT)
- Re: [AMBER] Use of pmemd for minimisation and equilibration (Fri Oct 27 2017 - 07:09:14 PDT)
- Re: [AMBER] RNA with ligand - a follow-up ANTECHAMBER question (Wed Oct 25 2017 - 19:35:50 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation (Tue Oct 24 2017 - 17:39:09 PDT)
- Re: [AMBER] Can we use OPLS force field in AMBER (Tue Oct 24 2017 - 06:34:59 PDT)
- Re: [AMBER] About penalty scores (Tue Oct 24 2017 - 05:09:55 PDT)
- Re: [AMBER] Force field parameters for Magnesium and Calcium in Amber (Fri Oct 20 2017 - 05:26:40 PDT)
- Re: [AMBER] effect of MPI problem on MD calculations (Fri Oct 20 2017 - 05:21:48 PDT)
- Re: [AMBER] Protein drift from solvent box (Thu Oct 19 2017 - 09:11:11 PDT)
- Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? (Thu Oct 19 2017 - 09:06:36 PDT)
- Re: [AMBER] Bias Towards the Periodic Boundary (Wed Oct 18 2017 - 13:03:02 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Mon Oct 16 2017 - 05:03:23 PDT)
- Re: [AMBER] Specify amount of memory (Sun Oct 15 2017 - 10:28:45 PDT)
- Re: [AMBER] pmemd.cuda and rigid CH2Cl2 (Sat Oct 14 2017 - 06:35:17 PDT)
- Re: [AMBER] problem with AMBER TUTORIAL A1 (Sat Oct 14 2017 - 06:31:18 PDT)
- Re: [AMBER] mdfrc for a single ion in vacuum (Fri Oct 13 2017 - 13:43:55 PDT)
- Re: [AMBER] help for the installation of Ambertools 17 on Mac (Fri Oct 13 2017 - 05:08:18 PDT)
- Re: [AMBER] Problem with charges - Unable to recover LYS charges from AmberFF (Wed Oct 11 2017 - 05:38:32 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Tue Oct 10 2017 - 06:55:29 PDT)
- Re: [AMBER] AMBER16 parallelisation and fftw3 error (Fri Oct 06 2017 - 05:08:24 PDT)
- Re: [AMBER] AmberTools17 and shape.h (Thu Oct 05 2017 - 10:53:04 PDT)
- Re: [AMBER] vague error when running constant ph simulations (Wed Oct 04 2017 - 05:44:57 PDT)
- Re: [AMBER] Is it possible to simulate Indium (coupled with sulpher and copper) nano material in amber? (Tue Oct 03 2017 - 10:15:49 PDT)
- Re: [AMBER] TImask command for PMEMD (Mon Oct 02 2017 - 14:26:26 PDT)
- Re: [AMBER] Amber16 electric field parameters (Mon Oct 02 2017 - 06:46:12 PDT)
- Re: [AMBER] Thermodynamic Integration with pmemd, for explicit solvent models (Sun Oct 01 2017 - 13:08:25 PDT)
David Cerutti
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Mon Oct 30 2017 - 13:21:06 PDT)
- Re: [AMBER] About paramfit 1-4 scaling (Wed Oct 25 2017 - 13:08:09 PDT)
- Re: [AMBER] force distribution analysis and Ewald (Tue Oct 03 2017 - 19:09:42 PDT)
David Sáez
- Re: [AMBER] Constant temperature is not constant from the beginning (Tue Oct 31 2017 - 14:31:22 PDT)
- [AMBER] Constant temperature is not constant from the beginning (Mon Oct 30 2017 - 21:32:29 PDT)
- [AMBER] Specify amount of memory (Sun Oct 15 2017 - 00:20:44 PDT)
Diego Gomes
- [AMBER] pdb4amber bug - incorrect "CONECT" between chains (Mon Oct 30 2017 - 10:49:33 PDT)
diego.soler.uam.es
- Re: [AMBER] Wham analysis (Sat Oct 14 2017 - 12:42:13 PDT)
Dow Hurst
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Mon Oct 30 2017 - 16:10:34 PDT)
Eiros Zamora, Juan
- [AMBER] Converting atom names from NAMD to AMBER (Fri Oct 13 2017 - 10:10:54 PDT)
Elvis Martis
- Re: [AMBER] Error in calculating MM-PBSA (Sun Oct 29 2017 - 03:34:10 PDT)
- Re: [AMBER] MM-PBSA calculation (Fri Oct 27 2017 - 08:53:02 PDT)
- Re: [AMBER] Binding affinity of different small molecules to a complex of metal + protein + DNA (Fri Oct 27 2017 - 08:06:07 PDT)
- Re: [AMBER] Use of pmemd for minimisation and equilibration (Fri Oct 27 2017 - 07:05:49 PDT)
- Re: [AMBER] difficulty reading a frcmod file in amber (Mon Oct 23 2017 - 02:24:27 PDT)
- Re: [AMBER] trajout format with cpptraj in Ambertools 17 (Tue Oct 17 2017 - 08:53:16 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Fri Oct 13 2017 - 01:01:54 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Thu Oct 12 2017 - 06:59:13 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Wed Oct 11 2017 - 02:25:21 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Wed Oct 11 2017 - 00:33:43 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Tue Oct 10 2017 - 06:09:39 PDT)
- Re: [AMBER] Independent MD runs (Wed Oct 04 2017 - 21:58:33 PDT)
- Re: [AMBER] total frames for hbond (Sun Oct 01 2017 - 20:30:15 PDT)
Eric Lang
- Re: [AMBER] Restarting pH-REMD simulations after abnormal termination (Fri Oct 13 2017 - 09:11:32 PDT)
- [AMBER] Restarting pH-REMD simulations after abnormal termination (Thu Oct 12 2017 - 06:55:28 PDT)
Eugene Cha
- [AMBER] difficulty reading a frcmod file in amber (Sun Oct 22 2017 - 23:41:42 PDT)
Feng Pan
- Re: [AMBER] How to put anchor_position for RMSD collective variable Value in string methods (Fri Oct 13 2017 - 09:06:52 PDT)
- Re: [AMBER] colvar in string methods (Wed Oct 04 2017 - 20:33:26 PDT)
FyD
- Re: [AMBER] PyRed (Mon Oct 02 2017 - 23:10:11 PDT)
George Tzotzos
- Re: [AMBER] Question on GPUs and OS (Mon Oct 16 2017 - 11:28:00 PDT)
- [AMBER] Question on GPUs and OS (Mon Oct 16 2017 - 11:15:38 PDT)
- Re: [AMBER] Vector math: a couple of questions (Wed Oct 04 2017 - 09:56:04 PDT)
- Re: [AMBER] Vector math: a couple of questions (Wed Oct 04 2017 - 09:43:20 PDT)
- [AMBER] Vector math: a couple of questions (Tue Oct 03 2017 - 11:42:09 PDT)
Gerald Monard
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Mon Oct 30 2017 - 14:29:33 PDT)
Goetz, Andreas
- Re: [AMBER] SCC-DFTB for iron (Tue Oct 31 2017 - 14:20:21 PDT)
Hai Nguyen
- Re: [AMBER] pdb4amber bug - incorrect "CONECT" between chains (Tue Oct 31 2017 - 06:12:11 PDT)
- Re: [AMBER] pdb4amber bug - incorrect "CONECT" between chains (Tue Oct 31 2017 - 05:39:30 PDT)
- Re: [AMBER] pdb4amber bug - incorrect "CONECT" between chains (Mon Oct 30 2017 - 20:21:27 PDT)
- Re: [AMBER] pdb4amber bug - incorrect "CONECT" between chains (Mon Oct 30 2017 - 19:46:32 PDT)
- Re: [AMBER] parmed.py and xparmed.py problem (Fri Oct 27 2017 - 06:06:06 PDT)
- Re: [AMBER] Forecefield error (Tue Oct 24 2017 - 20:20:26 PDT)
- Re: [AMBER] Forecefield error (Tue Oct 24 2017 - 20:09:53 PDT)
- Re: [AMBER] Are RNA with ligand system and a GB neck2 protocol compatible (Tue Oct 24 2017 - 19:31:20 PDT)
- Re: [AMBER] hydrogenbond calculations (Sun Oct 22 2017 - 21:53:36 PDT)
- Re: [AMBER] Question on GPUs and OS (Mon Oct 16 2017 - 11:20:50 PDT)
- Re: [AMBER] chamber is unavailable from terminal MacOS (Fri Oct 06 2017 - 15:31:18 PDT)
- Re: [AMBER] AMBER16 parallelisation and fftw3 error (Fri Oct 06 2017 - 14:25:32 PDT)
- Re: [AMBER] AmberTools17 and shape.h (Thu Oct 05 2017 - 17:28:56 PDT)
- Re: [AMBER] AMBER16 parallelisation and fftw3 error (Thu Oct 05 2017 - 15:57:17 PDT)
- Re: [AMBER] AMBER16 parallelisation and fftw3 error (Thu Oct 05 2017 - 15:20:47 PDT)
- Re: [AMBER] Current rmsd from reference in targeted MD (Tue Oct 03 2017 - 16:22:38 PDT)
Holger Kruse
- [AMBER] contributing code (Tue Oct 31 2017 - 06:19:43 PDT)
Hossein Geraili
- [AMBER] AMBER (Thu Oct 05 2017 - 02:44:50 PDT)
- Re: [AMBER] (no subject) (Thu Oct 05 2017 - 02:20:22 PDT)
huangwc8
- [AMBER] help for the installation of Ambertools 17 on Mac (Thu Oct 12 2017 - 22:40:50 PDT)
Hughes, Travis
- Re: [AMBER] trajout last x frames cpptraj (Mon Oct 02 2017 - 07:16:01 PDT)
jacob wick
- Re: [AMBER] Generating a dimer starting from monomers using MD (Thu Oct 05 2017 - 05:47:40 PDT)
- [AMBER] Generating a dimer starting from monomers using MD (Thu Oct 05 2017 - 02:26:48 PDT)
Jason Swails
- Re: [AMBER] Can we use OPLS force field in AMBER (Fri Oct 27 2017 - 04:56:54 PDT)
- Re: [AMBER] getting MC barostat to print less (Thu Oct 12 2017 - 19:36:26 PDT)
- Re: [AMBER] barostat with large coupling constant (Wed Oct 04 2017 - 12:58:20 PDT)
- Re: [AMBER] force distribution analysis and Ewald (Tue Oct 03 2017 - 12:37:44 PDT)
- Re: [AMBER] barostat with large coupling constant (Sun Oct 01 2017 - 20:37:57 PDT)
- Re: [AMBER] leaprc.constph and ff14sb (Sun Oct 01 2017 - 20:29:41 PDT)
Jeyaram R A
- [AMBER] STOP PMEMD Terminated Abnormally! (Thu Oct 26 2017 - 05:01:21 PDT)
Jian Yin
- Re: [AMBER] APR method in CHCl3 (Fri Oct 20 2017 - 14:02:53 PDT)
- Re: [AMBER] APR method in CHCl3 (Wed Oct 18 2017 - 13:51:34 PDT)
Junmei Wang
- Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 (Sat Oct 28 2017 - 18:02:13 PDT)
- Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 (Sat Oct 28 2017 - 06:23:26 PDT)
- Re: [AMBER] RNA with ligand - a follow-up ANTECHAMBER question (Thu Oct 26 2017 - 08:51:43 PDT)
- Re: [AMBER] Dr. Nick Riviera (Thu Oct 05 2017 - 08:47:29 PDT)
Karl Kirschner
- Re: [AMBER] Generating a dimer starting from monomers using MD (Thu Oct 05 2017 - 03:57:46 PDT)
Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] RNA with ligand - a follow-up ANTECHAMBER question (Thu Oct 26 2017 - 08:10:22 PDT)
- [AMBER] RNA with ligand - a follow-up ANTECHAMBER question (Wed Oct 25 2017 - 14:00:06 PDT)
- [AMBER] Are RNA with ligand system and a GB neck2 protocol compatible (Tue Oct 24 2017 - 10:57:29 PDT)
Khabiri, Morteza
- [AMBER] Thermodynamic integration/switch off/on cloumbic and vdw interactions (Fri Oct 06 2017 - 11:05:54 PDT)
Leena Aggarwal
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Mon Oct 16 2017 - 03:50:44 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 23:23:08 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 23:15:29 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 23:08:20 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 23:07:56 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 22:46:11 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 22:37:01 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 22:26:53 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 22:06:56 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Sun Oct 15 2017 - 21:38:15 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Thu Oct 12 2017 - 22:49:18 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Thu Oct 12 2017 - 05:12:51 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Thu Oct 12 2017 - 02:00:28 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Wed Oct 11 2017 - 21:24:17 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Wed Oct 11 2017 - 01:04:09 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Wed Oct 11 2017 - 00:11:12 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Wed Oct 11 2017 - 00:09:08 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Wed Oct 11 2017 - 00:03:36 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Tue Oct 10 2017 - 21:17:59 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation (Tue Oct 10 2017 - 06:47:19 PDT)
- [AMBER] query regarding the restart file of molecular dynamics simulation (Tue Oct 10 2017 - 05:40:03 PDT)
Li, Wen
- Re: [AMBER] trajout format with cpptraj in Ambertools 17 (Tue Oct 17 2017 - 10:57:26 PDT)
- Re: [AMBER] trajout format with cpptraj in Ambertools 17 (Tue Oct 17 2017 - 08:54:53 PDT)
- [AMBER] trajout format with cpptraj in Ambertools 17 (Tue Oct 17 2017 - 08:40:28 PDT)
- Re: [AMBER] parmstrip with cpptraj in Ambertools 17 (Fri Oct 13 2017 - 08:48:54 PDT)
- [AMBER] parmstrip with cpptraj in Ambertools 17 (Thu Oct 12 2017 - 10:12:37 PDT)
Lin Song
- Re: [AMBER] Center of mass restraint on GPU? (Fri Oct 20 2017 - 11:39:59 PDT)
- [AMBER] Center of mass restraint on GPU? (Fri Oct 20 2017 - 08:12:50 PDT)
Lizelle Lubbe
- Re: [AMBER] Independent production runs (Fri Oct 20 2017 - 05:44:53 PDT)
- [AMBER] Independent production runs (Fri Oct 20 2017 - 04:28:34 PDT)
- Re: [AMBER] Protein drift from solvent box (Fri Oct 20 2017 - 01:13:38 PDT)
- Re: [AMBER] Protein drift from solvent box (Thu Oct 19 2017 - 09:14:32 PDT)
- Re: [AMBER] Protein drift from solvent box (Thu Oct 19 2017 - 07:58:51 PDT)
- [AMBER] Protein drift from solvent box (Thu Oct 19 2017 - 05:44:48 PDT)
- [AMBER] Metal site hybrid bonded model (Fri Oct 13 2017 - 05:45:30 PDT)
M P
- [AMBER] positional restraint to optimize crystal structure (Mon Oct 30 2017 - 04:12:40 PDT)
Mac Kevin Braza
- [AMBER] Fwd: Error with AMBER/Charmm-GUI output (Mon Oct 09 2017 - 22:57:59 PDT)
- [AMBER] Fwd: Error with AMBER/Charmm-GUI output (Mon Oct 09 2017 - 22:57:33 PDT)
Marek Maly
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Mon Oct 30 2017 - 18:15:10 PDT)
- Re: [AMBER] DPPG lipid bilayer simulation using Lipid17 - too small area per lipid ? (Wed Oct 04 2017 - 16:44:02 PDT)
- [AMBER] DPPG lipid bilayer simulation using Lipid17 - too small area per lipid ? (Tue Oct 03 2017 - 08:52:41 PDT)
Maura Malinska
- [AMBER] APR method in CHCl3 (Wed Oct 18 2017 - 09:34:01 PDT)
megha vaishnavi
- [AMBER] hydrogenbond calculations (Sun Oct 22 2017 - 20:11:44 PDT)
Michael Shokhen
- [AMBER] disulfide bonds braking during MD simulation (Mon Oct 30 2017 - 05:23:00 PDT)
- Re: [AMBER] parmed.py and xparmed.py problem (Fri Oct 27 2017 - 06:40:18 PDT)
- [AMBER] parmed.py and xparmed.py problem (Fri Oct 27 2017 - 05:58:50 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation (Wed Oct 25 2017 - 14:05:50 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation (Wed Oct 25 2017 - 13:26:36 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation (Wed Oct 25 2017 - 12:39:14 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation (Wed Oct 25 2017 - 11:51:29 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation (Wed Oct 25 2017 - 11:37:47 PDT)
- Re: [AMBER] error with restraint distance minimization (Wed Oct 25 2017 - 09:31:00 PDT)
- [AMBER] error with restraint distance minimization (Wed Oct 25 2017 - 09:02:52 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation (Tue Oct 24 2017 - 08:50:17 PDT)
- [AMBER] disulfide bonds braking during MD simulation (Tue Oct 24 2017 - 07:59:52 PDT)
- Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? (Mon Oct 23 2017 - 06:51:58 PDT)
- Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? (Thu Oct 19 2017 - 07:27:17 PDT)
- [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? (Thu Oct 19 2017 - 05:42:38 PDT)
- [AMBER] problem with AMBER TUTORIAL A1 (Fri Oct 13 2017 - 05:27:12 PDT)
Miha Purg
- Re: [AMBER] MCPB.py issue - add_bonded_pairs (Mon Oct 09 2017 - 10:53:04 PDT)
mirzo
- Re: [AMBER] parmed.py and xparmed.py problem (Fri Oct 27 2017 - 06:36:29 PDT)
Mustafa Alhaji Isa
- [AMBER] Error in calculating MM-PBSA (Sun Oct 29 2017 - 01:11:59 PDT)
- [AMBER] MM-PBSA calculation (Fri Oct 27 2017 - 08:22:33 PDT)
Nadine Schwierz-Neumann
- [AMBER] Force field parameters for Magnesium and Calcium in Amber (Fri Oct 20 2017 - 03:35:06 PDT)
Nicolas Cheron
- Re: [AMBER] Problem with charges - Unable to recover LYS charges from AmberFF (Mon Oct 16 2017 - 00:50:46 PDT)
- [AMBER] Problem with charges - Unable to recover LYS charges from AmberFF (Wed Oct 11 2017 - 03:13:59 PDT)
Niel Henriksen
- Re: [AMBER] WHAM, DHAM, MBAR, BAR, TI... (Thu Oct 19 2017 - 12:24:19 PDT)
- [AMBER] SCEE incorrectly set for certain dihedral parameter comments (Fri Oct 13 2017 - 12:05:00 PDT)
Pacheco, Sayuri
- Re: [AMBER] Running Explicit pH MD (Mon Oct 30 2017 - 08:20:52 PDT)
- [AMBER] Running Explicit pH MD (Mon Oct 30 2017 - 07:31:36 PDT)
- Re: [AMBER] Running Explicit pH MD (Tue Oct 24 2017 - 21:54:54 PDT)
- [AMBER] Running Explicit pH MD (Mon Oct 16 2017 - 08:26:33 PDT)
- [AMBER] Constant pH Explicit Solvent (Wed Oct 04 2017 - 18:22:18 PDT)
Parthiban Marimuthu
- Re: [AMBER] System preparation for protein with Multiple Zn-CCCC (Sat Oct 07 2017 - 13:58:49 PDT)
- [AMBER] System preparation for protein with Multiple Zn-CCCC (Fri Oct 06 2017 - 09:16:07 PDT)
Paul Freidhoff
- [AMBER] Dummy Atoms in CP (Thu Oct 19 2017 - 06:34:57 PDT)
- [AMBER] Question regarding protonated CP in pH dependent REMD (Mon Oct 09 2017 - 09:04:09 PDT)
Pengfei Li
- Re: [AMBER] Cannot create Ru-ligands bonds using genMetalFF.sh (Wed Oct 18 2017 - 09:21:34 PDT)
- Re: [AMBER] Cannot create Ru-ligands bonds using genMetalFF.sh (Wed Oct 18 2017 - 09:19:19 PDT)
- Re: [AMBER] System preparation for protein with Multiple Zn-CCCC (Thu Oct 12 2017 - 19:59:28 PDT)
- Re: [AMBER] MCPB.py issue - add_bonded_pairs (Thu Oct 12 2017 - 19:53:18 PDT)
- Re: [AMBER] Error reading Ruthenium complex residue (Thu Oct 12 2017 - 19:47:11 PDT)
- Re: [AMBER] Error in preparation of Zn.lib (Fri Oct 06 2017 - 07:45:49 PDT)
- Re: [AMBER] Amber16 electric field parameters (Thu Oct 05 2017 - 18:15:47 PDT)
- Re: [AMBER] Amber16 electric field parameters (Tue Oct 03 2017 - 19:10:00 PDT)
Pietro Aronica
- Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? (Thu Oct 19 2017 - 06:44:17 PDT)
- Re: [AMBER] Vector command in cpptraj (Mon Oct 16 2017 - 20:39:44 PDT)
- [AMBER] Vector command in cpptraj (Sun Oct 15 2017 - 21:14:22 PDT)
R zu
- Re: [AMBER] barostat with large coupling constant (Wed Oct 04 2017 - 09:16:53 PDT)
- Re: [AMBER] barostat with large coupling constant (Wed Oct 04 2017 - 08:49:22 PDT)
Rana Rehan Khalid
- Re: [AMBER] Error Due to Duplicate residues atoms (Sat Oct 28 2017 - 09:31:48 PDT)
- [AMBER] Error Due to Duplicate residues atoms (Fri Oct 27 2017 - 11:15:16 PDT)
- Re: [AMBER] how we can visualized the bonds after saving on of the MD frame into pdb file. (Thu Oct 19 2017 - 11:22:46 PDT)
- [AMBER] how we can visualized the bonds after saving on of the MD frame into pdb file. (Thu Oct 19 2017 - 11:16:51 PDT)
- [AMBER] How to show double bond connection between N=O2 (Sat Oct 14 2017 - 07:31:29 PDT)
- Re: [AMBER] output file .out file deleted mistakenly (Wed Oct 11 2017 - 11:13:49 PDT)
- [AMBER] output file .out file deleted mistakenly (Wed Oct 11 2017 - 10:35:48 PDT)
Ray Luo
- Re: [AMBER] MMPBSA error (Wed Oct 11 2017 - 07:58:55 PDT)
- Re: [AMBER] MMPBSA error (Mon Oct 09 2017 - 20:20:37 PDT)
Robert Molt
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Mon Oct 30 2017 - 12:59:43 PDT)
Robin Betz
- Re: [AMBER] about Paramfit (Fri Oct 06 2017 - 14:22:43 PDT)
Rodrigo Galindo-Murillo
- Re: [AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ (Mon Oct 30 2017 - 06:25:58 PDT)
Roma Mukhopadhyay
- [AMBER] TI calculations using pmemd (Wed Oct 04 2017 - 13:00:22 PDT)
- [AMBER] TImask command for PMEMD (Mon Oct 02 2017 - 10:01:12 PDT)
- Re: [AMBER] Thermodynamic Integration with pmemd, for explicit solvent models (Sun Oct 01 2017 - 16:54:40 PDT)
- [AMBER] Thermodynamic Integration with pmemd, for explicit solvent models (Sat Sep 30 2017 - 19:48:47 PDT)
Ross Walker
- Re: [AMBER] CUDA 9 (Tue Oct 31 2017 - 10:53:58 PDT)
- [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Mon Oct 30 2017 - 11:57:47 PDT)
- Re: [AMBER] Use of pmemd for minimisation and equilibration (Fri Oct 27 2017 - 08:06:34 PDT)
- Re: [AMBER] Center of mass restraint on GPU? (Fri Oct 20 2017 - 10:28:31 PDT)
- Re: [AMBER] Amber16 electric field parameters (Mon Oct 02 2017 - 06:52:14 PDT)
Sanaa ALAbbad
- Re: [AMBER] Cannot create Ru-ligands bonds using genMetalFF.sh (Thu Oct 19 2017 - 06:39:47 PDT)
- Re: [AMBER] Cannot create Ru-ligands bonds using genMetalFF.sh (Wed Oct 18 2017 - 17:14:09 PDT)
- [AMBER] Cannot create Ru-ligands bonds using genMetalFF.sh (Tue Oct 17 2017 - 16:10:44 PDT)
- Re: [AMBER] Error reading Ruthenium complex residue (Fri Oct 13 2017 - 06:18:03 PDT)
- Re: [AMBER] Error reading Ruthenium complex residue (Thu Oct 12 2017 - 09:56:11 PDT)
- [AMBER] Error reading Ruthenium complex residue (Thu Oct 12 2017 - 08:27:17 PDT)
- Re: [AMBER] Ruthenium complex MD simulation ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported! (Mon Oct 09 2017 - 16:52:01 PDT)
- [AMBER] Ruthenium complex MD simulation ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported! (Mon Oct 09 2017 - 16:44:24 PDT)
sangita kachhap
- Re: [AMBER] restraint_wt applied to wrong atoms (Mon Oct 30 2017 - 06:02:50 PDT)
- [AMBER] restraint_wt applied to wrong atoms (Mon Oct 30 2017 - 05:14:11 PDT)
- Re: [AMBER] MM/PBSA or MM/GBSA (Tue Oct 24 2017 - 12:46:57 PDT)
- Re: [AMBER] MM/PBSA or MM/GBSA (Tue Oct 24 2017 - 07:00:07 PDT)
- [AMBER] MM/PBSA or MM/GBSA (Tue Oct 24 2017 - 06:47:21 PDT)
- [AMBER] effect of MPI problem on MD calculations (Fri Oct 20 2017 - 01:25:20 PDT)
- Re: [AMBER] MMPBSA error (Wed Oct 11 2017 - 03:37:25 PDT)
- [AMBER] MMPBSA error (Mon Oct 09 2017 - 07:27:26 PDT)
Scott Le Grand
- Re: [AMBER] CUDA 9 (Tue Oct 31 2017 - 12:36:33 PDT)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Tue Oct 31 2017 - 08:30:51 PDT)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER (Mon Oct 30 2017 - 12:29:30 PDT)
Seth Axen
- Re: [AMBER] RESP charges for a peptide-bound probe with R.E.D. (Tue Oct 17 2017 - 08:54:39 PDT)
- [AMBER] RESP charges for a peptide-bound probe with R.E.D. (Mon Oct 16 2017 - 16:00:30 PDT)
Setyanto Md
- Re: [AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ (Mon Oct 30 2017 - 07:07:55 PDT)
- [AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ (Mon Oct 30 2017 - 05:16:23 PDT)
Sharon D. Morris
- [AMBER] positive electrostatic energy (Mon Oct 30 2017 - 03:35:18 PDT)
Shilpa Gupta
- [AMBER] warning Close contact (Mon Oct 30 2017 - 03:56:13 PDT)
- [AMBER] AM1-BCC for charge derivation (Sun Oct 29 2017 - 12:22:40 PDT)
- Re: [AMBER] Can we use OPLS force field in AMBER (Tue Oct 24 2017 - 21:06:17 PDT)
- Re: [AMBER] Can we use OPLS force field in AMBER (Tue Oct 24 2017 - 06:57:11 PDT)
- [AMBER] Can we use OPLS force field in AMBER (Tue Oct 24 2017 - 05:35:52 PDT)
Shirin Jamshidi
- Re: [AMBER] AMBER16 parallelisation and fftw3 error (Fri Oct 06 2017 - 14:45:02 PDT)
- Re: [AMBER] AMBER16 parallelisation and fftw3 error (Fri Oct 06 2017 - 06:37:20 PDT)
- Re: [AMBER] AMBER16 parallelisation and fftw3 error (Fri Oct 06 2017 - 04:24:57 PDT)
- Re: [AMBER] AMBER16 parallelisation and fftw3 error (Thu Oct 05 2017 - 15:24:08 PDT)
- [AMBER] AMBER16 parallelisation and fftw3 error (Thu Oct 05 2017 - 14:41:57 PDT)
Smith, Louis
- Re: [AMBER] getting MC barostat to print less (Thu Oct 12 2017 - 22:14:25 PDT)
- [AMBER] getting MC barostat to print less (Wed Oct 11 2017 - 21:36:58 PDT)
Sonia Ziada
- Re: [AMBER] Current rmsd from reference in targeted MD (Wed Oct 04 2017 - 08:16:55 PDT)
- Re: [AMBER] Current rmsd from reference in targeted MD (Wed Oct 04 2017 - 05:45:34 PDT)
- Re: [AMBER] Current rmsd from reference in targeted MD (Wed Oct 04 2017 - 05:25:36 PDT)
- Re: [AMBER] Current rmsd from reference in targeted MD (Wed Oct 04 2017 - 00:10:11 PDT)
- Re: [AMBER] Current rmsd from reference in targeted MD (Tue Oct 03 2017 - 14:05:04 PDT)
- [AMBER] Current rmsd from reference in targeted MD (Tue Oct 03 2017 - 04:36:33 PDT)
Suchetana Gupta
- [AMBER] Use of pmemd for minimisation and equilibration (Fri Oct 27 2017 - 05:52:56 PDT)
Sundar
- [AMBER] striping correctly with ante-MMPBSA.py (Mon Oct 09 2017 - 01:24:38 PDT)
- [AMBER] chamber is unavailable from terminal MacOS (Fri Oct 06 2017 - 15:02:47 PDT)
Szymon Żaczek
- Re: [AMBER] Error reading Ruthenium complex residue (Thu Oct 12 2017 - 09:51:35 PDT)
- Re: [AMBER] MCPB.py issue - add_bonded_pairs (Mon Oct 09 2017 - 13:00:18 PDT)
- [AMBER] MCPB.py issue - add_bonded_pairs (Mon Oct 09 2017 - 08:37:38 PDT)
Thakur, Abhishek
- Re: [AMBER] Protein drift from solvent box (Thu Oct 19 2017 - 07:06:42 PDT)
- [AMBER] Wham analysis (Fri Oct 13 2017 - 07:32:40 PDT)
- [AMBER] Wham analysis (Thu Oct 12 2017 - 14:02:35 PDT)
- [AMBER] total frames for hbond (Sun Oct 01 2017 - 12:16:42 PDT)
Thomas Cheatham
- Re: [AMBER] Binding affinity of different small molecules to a complex of metal + protein + DNA (Fri Oct 27 2017 - 15:20:03 PDT)
Thomas Pochapsky
- [AMBER] force distribution analysis and Ewald (Tue Oct 03 2017 - 11:57:01 PDT)
Timothy Schutt
- Re: [AMBER] Bias Towards the Periodic Boundary (Wed Oct 18 2017 - 13:11:43 PDT)
- [AMBER] Bias Towards the Periodic Boundary (Wed Oct 18 2017 - 10:37:56 PDT)
Urszula Uciechowska
- [AMBER] PB Bomb in pb_aaradi() (Tue Oct 31 2017 - 06:41:15 PDT)
Weinzierl, Robert O J
- [AMBER] CUDA 9 (Tue Oct 31 2017 - 10:11:52 PDT)
William Marquardt
- [AMBER] mdfrc for a single ion in vacuum (Fri Oct 13 2017 - 11:24:46 PDT)
Wook Lee
- [AMBER] reference for long-range van der Waals interactions (Thu Oct 26 2017 - 08:16:06 PDT)
Xibing He
- [AMBER] net charge problem of Amber Lipid14 Force Field (Thu Oct 05 2017 - 15:03:47 PDT)
Àngels González Lafont
- [AMBER] SCC-DFTB for iron (Tue Oct 31 2017 - 09:04:43 PDT)

Amber Archive Oct 2017 by author