Amber Archive Oct 2019 by author
378 messages
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Starting
Mon Sep 30 2019 - 20:00:02 PDT,
Ending
Thu Oct 31 2019 - 06:00:02 PDT
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Aiden Aceves
Re: [AMBER] Multiple simulations on one GPU
(Wed Oct 30 2019 - 07:27:54 PDT)
[AMBER] Multiple simulations on one GPU
(Tue Oct 29 2019 - 08:55:12 PDT)
Airy Sanjeev
[AMBER] Problem in the x-axis of SASA analysis
(Mon Oct 28 2019 - 22:47:03 PDT)
[AMBER] Extract the last 90ns trajectory
(Wed Oct 23 2019 - 02:29:14 PDT)
Re: [AMBER] Problem in running MMPBSA
(Wed Oct 16 2019 - 02:47:10 PDT)
[AMBER] Problem in running MMPBSA
(Wed Oct 16 2019 - 02:23:43 PDT)
[AMBER] Problem in extracting pdb file from mdcrd file
(Mon Oct 14 2019 - 01:07:15 PDT)
Akinpelu Olayinka
Re: [AMBER] Error in Step two of MCPB
(Wed Oct 30 2019 - 06:23:22 PDT)
Alen Ahmetovic
Re: [AMBER] make install errors
(Tue Oct 29 2019 - 16:49:24 PDT)
Re: [AMBER] make install errors
(Wed Oct 16 2019 - 15:44:52 PDT)
Re: [AMBER] make install errors
(Wed Oct 16 2019 - 15:34:49 PDT)
[AMBER] make install errors
(Mon Oct 14 2019 - 19:28:33 PDT)
Andrea H. Kasun
Re: [AMBER] iwrap
(Tue Oct 22 2019 - 03:55:21 PDT)
[AMBER] iwrap
(Tue Oct 22 2019 - 03:11:50 PDT)
Anthony Cruz-Balberdy
Re: [AMBER] "Could not import Amber Python modules!" error
(Wed Oct 09 2019 - 06:47:11 PDT)
Anuja Ware
[AMBER] Convergence value for GMAX
(Thu Oct 17 2019 - 06:48:53 PDT)
Aravind R
[AMBER] Force extension curve from ASMD
(Mon Oct 07 2019 - 00:27:12 PDT)
Bill Ross
Re: [AMBER] Problem in Leap PDB Reading
(Wed Oct 23 2019 - 21:53:37 PDT)
Re: [AMBER] How to obtain the pressure in NVT ensemble
(Tue Oct 22 2019 - 00:44:00 PDT)
Re: [AMBER] NAN error
(Mon Oct 21 2019 - 14:22:50 PDT)
Re: [AMBER] NAN error
(Mon Oct 21 2019 - 08:01:50 PDT)
Re: [AMBER] NAN error
(Mon Oct 21 2019 - 06:45:48 PDT)
Re: [AMBER] NAN error
(Mon Oct 21 2019 - 06:17:54 PDT)
Re: [AMBER] Problem with installation of AMBER
(Mon Oct 21 2019 - 05:38:15 PDT)
Re: [AMBER] minimize protein with a small molecule tethered at a fixed location
(Wed Oct 16 2019 - 06:47:21 PDT)
Re: [AMBER] minimize protein with a small molecule tethered at a fixed location
(Wed Oct 16 2019 - 06:34:58 PDT)
Re: [AMBER] Problem in running MMPBSA
(Wed Oct 16 2019 - 02:34:47 PDT)
Re: [AMBER] Paste command for xleap
(Tue Oct 15 2019 - 06:17:09 PDT)
Re: [AMBER] Cataline
(Mon Oct 14 2019 - 00:34:38 PDT)
Re: [AMBER] Cataline
(Sun Oct 13 2019 - 14:52:55 PDT)
Re: [AMBER] Trouble Installing Amber on Mac
(Sat Oct 12 2019 - 00:23:09 PDT)
Re: [AMBER] Trouble Installing Amber on Mac
(Fri Oct 11 2019 - 22:31:39 PDT)
Re: [AMBER] tleap changes order of atoms in the parm file
(Thu Oct 10 2019 - 11:48:34 PDT)
Re: [AMBER] tleap changes order of atoms in the parm file
(Thu Oct 10 2019 - 07:46:50 PDT)
Re: [AMBER] tleap changes order of atoms in the parm file
(Thu Oct 10 2019 - 07:13:08 PDT)
Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom
(Wed Oct 09 2019 - 02:03:51 PDT)
Re: [AMBER] tleap hangs when tries to read new residue
(Mon Oct 07 2019 - 02:52:14 PDT)
Re: [AMBER] How can I use modified GAFF?
(Mon Oct 07 2019 - 01:00:51 PDT)
Re: [AMBER] How can I use modified GAFF?
(Mon Oct 07 2019 - 00:59:25 PDT)
Re: [AMBER] tleap hangs when tries to read new residue
(Sun Oct 06 2019 - 12:49:51 PDT)
Re: [AMBER] tleap hangs when tries to read new residue
(Sun Oct 06 2019 - 12:48:28 PDT)
Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop
(Thu Oct 03 2019 - 23:37:51 PDT)
Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop
(Thu Oct 03 2019 - 02:09:12 PDT)
Re: [AMBER] I add Ions to the system and they don't show up!!!
(Wed Oct 02 2019 - 17:08:58 PDT)
Carlos Simmerling
Re: [AMBER] REMD Error
(Tue Oct 29 2019 - 10:35:08 PDT)
Re: [AMBER] if the ligand doesn't bind when it should, what does it say about quality of my simulations and what can I do?
(Tue Oct 29 2019 - 10:33:46 PDT)
Re: [AMBER] REMD Error
(Mon Oct 28 2019 - 07:23:07 PDT)
Re: [AMBER] REMD Error
(Sat Oct 26 2019 - 04:33:43 PDT)
Re: [AMBER] REMD Error
(Sat Oct 26 2019 - 03:26:35 PDT)
Re: [AMBER] REMD Error
(Fri Oct 25 2019 - 12:33:46 PDT)
Re: [AMBER] Lennard-Jones parameters in amber and gromacs
(Thu Oct 24 2019 - 09:55:02 PDT)
Re: [AMBER] Combining FF14Sb and ForceField_PTM (FF03)... What could possibly go wrong?
(Wed Oct 23 2019 - 15:28:22 PDT)
Re: [AMBER] Extract the last 90ns trajectory
(Wed Oct 23 2019 - 03:10:59 PDT)
Re: [AMBER] constraining ligands to some distance from a target molecule on pmemd.cuda
(Tue Oct 22 2019 - 14:01:53 PDT)
Re: [AMBER] iwrap
(Tue Oct 22 2019 - 03:21:48 PDT)
Re: [AMBER] Calculate MMGBSA keeping water in binding site
(Mon Oct 21 2019 - 05:48:24 PDT)
Re: [AMBER] more efficient TI rerun over existing trajectory
(Thu Oct 17 2019 - 10:44:04 PDT)
Re: [AMBER] more efficient TI rerun over existing trajectory
(Thu Oct 17 2019 - 03:54:45 PDT)
Re: [AMBER] What is the correction in amber99SB-*-ILDN?
(Fri Oct 11 2019 - 08:29:08 PDT)
Re: [AMBER] Calculate MMGBSA keeping water in binding site
(Thu Oct 10 2019 - 11:06:05 PDT)
Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom
(Tue Oct 08 2019 - 12:01:05 PDT)
Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom
(Tue Oct 08 2019 - 11:46:37 PDT)
Re: [AMBER] amber99sb-disp forcefield in Amber
(Tue Oct 08 2019 - 11:40:36 PDT)
Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom
(Tue Oct 08 2019 - 10:33:18 PDT)
Re: [AMBER] Question about ff14SB and parameter files
(Mon Oct 07 2019 - 18:09:20 PDT)
Re: [AMBER] Calculate MMGBSA keeping water in binding site
(Fri Oct 04 2019 - 06:35:40 PDT)
Re: [AMBER] regarding amber licensed version and free version.
(Tue Oct 01 2019 - 09:09:55 PDT)
Cavender, Chapin
[AMBER] Incorrect instructions in tutorial B1
(Wed Oct 16 2019 - 16:23:27 PDT)
Charles Lin
Re: [AMBER] more efficient TI rerun over existing trajectory
(Thu Oct 17 2019 - 07:37:35 PDT)
Re: [AMBER] Thermodynamic integration
(Thu Oct 17 2019 - 07:26:50 PDT)
Re: [AMBER] Thermodynamic integration
(Mon Oct 14 2019 - 13:03:26 PDT)
Re: [AMBER] Thermodynamic integration
(Mon Oct 14 2019 - 09:58:35 PDT)
Re: [AMBER] Thermodynamic integration
(Mon Oct 14 2019 - 07:20:10 PDT)
Re: [AMBER] Thermodynamic integration
(Thu Oct 10 2019 - 11:51:20 PDT)
Re: [AMBER] Thermodynamic integration
(Thu Oct 10 2019 - 06:13:11 PDT)
Re: [AMBER] Thermodynamic integration
(Thu Oct 03 2019 - 12:23:16 PDT)
Re: [AMBER] Thermodynamic integration
(Thu Oct 03 2019 - 09:15:51 PDT)
Re: [AMBER] Thermodynamic integration
(Thu Oct 03 2019 - 09:13:44 PDT)
Re: [AMBER] Thermodynamic integration
(Wed Oct 02 2019 - 08:19:52 PDT)
Charles-Alexandre Mattelaer
Re: [AMBER] sander/lmod parallel execution
(Tue Oct 22 2019 - 00:39:09 PDT)
[AMBER] sander/lmod parallel execution
(Mon Oct 21 2019 - 07:07:29 PDT)
Re: [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ?
(Sun Oct 06 2019 - 23:01:19 PDT)
Re: [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ?
(Sat Oct 05 2019 - 14:11:52 PDT)
[AMBER] Gtx 16-series
(Wed Oct 02 2019 - 09:40:51 PDT)
chaumont
[AMBER] Gaff v2.1 Force Field for n4
(Tue Oct 08 2019 - 05:29:45 PDT)
Chetna Tyagi
Re: [AMBER] How to incorporate new lipid molecules through packmol-memgen
(Tue Oct 01 2019 - 02:54:35 PDT)
Chuan Tian
Re: [AMBER] ff19SB update
(Wed Oct 16 2019 - 07:04:06 PDT)
Daniel Roe
Re: [AMBER] atomicfluct/rmsf time
(Wed Oct 30 2019 - 07:18:25 PDT)
Re: [AMBER] compiling Amber with gcc 9.2 and intel mpi 2019
(Wed Oct 30 2019 - 07:03:59 PDT)
Re: [AMBER] Problem in the x-axis of SASA analysis
(Wed Oct 30 2019 - 06:56:06 PDT)
Re: [AMBER] Extract the last 90ns trajectory
(Wed Oct 23 2019 - 10:12:50 PDT)
Re: [AMBER] clustering using distance matrix file only
(Tue Oct 22 2019 - 05:55:23 PDT)
Re: [AMBER] Problem in extracting pdb file from mdcrd file
(Wed Oct 16 2019 - 07:48:28 PDT)
Re: [AMBER] Error during the test of amber 18 installation
(Thu Oct 10 2019 - 09:06:57 PDT)
Re: [AMBER] H - bond tools
(Thu Oct 10 2019 - 08:00:03 PDT)
Re: [AMBER] CPPTRAJ parameter file error
(Thu Oct 10 2019 - 07:16:33 PDT)
Re: [AMBER] cpptraj.MPI error
(Mon Oct 07 2019 - 12:42:46 PDT)
Re: [AMBER] CPPTRAJ parameter file error
(Mon Oct 07 2019 - 07:47:13 PDT)
Re: [AMBER] Rotational/torsion energy
(Thu Oct 03 2019 - 12:33:08 PDT)
Re: [AMBER] Error during the test of amber 18 installation
(Thu Oct 03 2019 - 10:49:53 PDT)
Re: [AMBER] CPPTRAJ parameter file error
(Thu Oct 03 2019 - 05:42:13 PDT)
Re: [AMBER] ERROR: NaNs found in input coordinates.
(Thu Oct 03 2019 - 05:37:58 PDT)
Re: [AMBER] CPPTRAJ parameter file error
(Wed Oct 02 2019 - 06:31:48 PDT)
Re: [AMBER] I add Ions to the system and they don't show up!!!
(Tue Oct 01 2019 - 10:01:36 PDT)
Re: [AMBER] netcdf: issue with timestamp
(Tue Oct 01 2019 - 09:59:41 PDT)
David A Case
Re: [AMBER] Some short Catalina experience
(Tue Oct 29 2019 - 05:59:41 PDT)
Re: [AMBER] more efficient TI rerun over existing trajectory
(Tue Oct 29 2019 - 05:42:47 PDT)
Re: [AMBER] Problem in the x-axis of SASA analysis
(Tue Oct 29 2019 - 05:32:45 PDT)
Re: [AMBER] compiling Amber with gcc 9.2 and intel mpi 2019
(Mon Oct 28 2019 - 11:48:46 PDT)
Re: [AMBER] Problem in Leap PDB Reading
(Fri Oct 25 2019 - 09:09:18 PDT)
Re: [AMBER] TI on gpus
(Fri Oct 25 2019 - 08:59:58 PDT)
Re: [AMBER] NAN error
(Wed Oct 23 2019 - 05:01:17 PDT)
Re: [AMBER] free energy calculation and leap error
(Tue Oct 22 2019 - 11:20:23 PDT)
Re: [AMBER] thermodynamic integration parameters in input file
(Tue Oct 22 2019 - 11:17:23 PDT)
Re: [AMBER] Error adding OH⁻ ions in a simulation box
(Tue Oct 22 2019 - 05:42:47 PDT)
Re: [AMBER] iwrap
(Tue Oct 22 2019 - 05:34:24 PDT)
Re: [AMBER] error while running pmemd.cuda after reinstallation of amber 16
(Tue Oct 22 2019 - 05:16:30 PDT)
Re: [AMBER] How to obtain the pressure in NVT ensemble
(Tue Oct 22 2019 - 05:03:32 PDT)
Re: [AMBER] Problem with installation of AMBER
(Mon Oct 21 2019 - 05:30:20 PDT)
Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew
(Fri Oct 18 2019 - 08:13:07 PDT)
Re: [AMBER] ff19SB update
(Fri Oct 18 2019 - 06:49:50 PDT)
[AMBER] Some short Catalina experience
(Thu Oct 17 2019 - 10:49:13 PDT)
Re: [AMBER] Convergence value for GMAX
(Thu Oct 17 2019 - 10:36:04 PDT)
Re: [AMBER] Check for updates failed
(Thu Oct 17 2019 - 06:02:23 PDT)
Re: [AMBER] minimization using restrain weight
(Wed Oct 16 2019 - 07:56:53 PDT)
Re: [AMBER] ff19SB update
(Wed Oct 16 2019 - 07:51:14 PDT)
Re: [AMBER] Problem in running MMPBSA
(Wed Oct 16 2019 - 05:27:13 PDT)
Re: [AMBER] minimize protein with a small molecule tethered at a fixed location
(Wed Oct 16 2019 - 05:22:46 PDT)
Re: [AMBER] More ... problems in compilation: fftw3a | Case2 - Using intel
(Tue Oct 15 2019 - 05:05:12 PDT)
Re: [AMBER] Cataline
(Mon Oct 14 2019 - 05:52:25 PDT)
Re: [AMBER] What is the correction in amber99SB-*-ILDN?
(Mon Oct 14 2019 - 05:40:09 PDT)
Re: [AMBER] Trouble Installing Amber on Mac
(Mon Oct 14 2019 - 05:25:11 PDT)
Re: [AMBER] Query regarding DNA
(Fri Oct 11 2019 - 10:31:52 PDT)
Re: [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber
(Fri Oct 11 2019 - 07:24:45 PDT)
Re: [AMBER] tleap changes order of atoms in the parm file
(Thu Oct 10 2019 - 09:50:54 PDT)
Re: [AMBER] "Could not import Amber Python modules!" error
(Wed Oct 09 2019 - 08:30:19 PDT)
Re: [AMBER] Imaging issue
(Tue Oct 08 2019 - 04:49:53 PDT)
Re: [AMBER] Error during the test of amber 18 installation
(Mon Oct 07 2019 - 05:26:29 PDT)
Re: [AMBER] Error during the test of amber 18 installation
(Mon Oct 07 2019 - 05:25:35 PDT)
Re: [AMBER] tleap hangs when tries to read new residue
(Mon Oct 07 2019 - 05:21:41 PDT)
Re: [AMBER] Amber Installation Problem on Mac: update
(Fri Oct 04 2019 - 09:17:08 PDT)
Re: [AMBER] Amber Installation Problem on Mac
(Fri Oct 04 2019 - 07:10:13 PDT)
David Case
Re: [AMBER] make install errors
(Tue Oct 29 2019 - 18:59:16 PDT)
Re: [AMBER] Assigning am1-bcc charges to a whole library of ligands
(Sun Oct 27 2019 - 19:12:13 PDT)
Re: [AMBER] atomicfluct/rmsf time
(Sat Oct 26 2019 - 05:11:16 PDT)
Re: [AMBER] Problem with Installation of AMBER
(Sat Oct 19 2019 - 09:46:51 PDT)
Re: [AMBER] Some short Catalina experience
(Thu Oct 17 2019 - 18:42:18 PDT)
Re: [AMBER] Check for updates failed
(Wed Oct 16 2019 - 19:31:03 PDT)
Re: [AMBER] Cataline
(Wed Oct 16 2019 - 19:19:16 PDT)
[AMBER] Adding OH- to a water box
(Sun Oct 13 2019 - 05:16:49 PDT)
Re: [AMBER] Problems in compilation: fftw3.a ??
(Sat Oct 12 2019 - 05:22:38 PDT)
Re: [AMBER] Adding OH⁻ in a water box
(Fri Oct 11 2019 - 18:45:12 PDT)
Re: [AMBER] About STOP PMEMD Terminated Abnormally!
(Sat Oct 05 2019 - 05:58:36 PDT)
Re: [AMBER] Thermodynamic integration
(Thu Oct 03 2019 - 12:59:54 PDT)
Re: [AMBER] Error during the test of amber 18 installation
(Wed Oct 02 2019 - 12:02:34 PDT)
Re: [AMBER] WHere do I modify the charge of a standard residue?
(Wed Oct 02 2019 - 11:48:03 PDT)
Re: [AMBER] I add Ions to the system and they don't show up!!!
(Tue Oct 01 2019 - 18:07:05 PDT)
David Cerutti
Re: [AMBER] Multiple simulations on one GPU
(Tue Oct 29 2019 - 10:46:10 PDT)
Re: [AMBER] Problems in compilation: fftw3.a ??
(Fri Oct 11 2019 - 13:12:49 PDT)
David Ricardo Figueroa Blanco
[AMBER] PARMFIT and CHARMM
(Thu Oct 24 2019 - 12:55:47 PDT)
David Sáez
[AMBER] WHere do I modify the charge of a standard residue?
(Wed Oct 02 2019 - 06:42:54 PDT)
[AMBER] Is there any standard set of parameters to build the topology Iron Sulfur clusters?
(Tue Oct 01 2019 - 06:37:24 PDT)
Dawid das
Re: [AMBER] What is the correction in amber99SB-*-ILDN?
(Sat Oct 12 2019 - 09:33:06 PDT)
[AMBER] What is the correction in amber99SB-*-ILDN?
(Fri Oct 11 2019 - 08:23:57 PDT)
Re: [AMBER] tleap changes order of atoms in the parm file
(Thu Oct 10 2019 - 08:14:53 PDT)
Re: [AMBER] tleap changes order of atoms in the parm file
(Thu Oct 10 2019 - 07:36:12 PDT)
[AMBER] tleap changes order of atoms in the parm file
(Thu Oct 10 2019 - 07:09:16 PDT)
Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom
(Wed Oct 09 2019 - 02:05:55 PDT)
Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom
(Wed Oct 09 2019 - 01:54:52 PDT)
Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom
(Tue Oct 08 2019 - 11:58:29 PDT)
Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom
(Tue Oct 08 2019 - 11:00:25 PDT)
[AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom
(Tue Oct 08 2019 - 09:03:59 PDT)
Re: [AMBER] tleap hangs when tries to read new residue
(Mon Oct 07 2019 - 14:52:30 PDT)
Re: [AMBER] tleap hangs when tries to read new residue
(Mon Oct 07 2019 - 05:31:01 PDT)
Re: [AMBER] tleap hangs when tries to read new residue
(Mon Oct 07 2019 - 02:40:27 PDT)
[AMBER] tleap hangs when tries to read new residue
(Sun Oct 06 2019 - 10:09:05 PDT)
Debarati DasGupta
[AMBER] Any ideas what may be wrong
(Thu Oct 31 2019 - 05:58:19 PDT)
[AMBER] Thermodynamic integration questions questions and questions
(Tue Oct 29 2019 - 08:59:12 PDT)
Re: [AMBER] TI on gpus
(Fri Oct 25 2019 - 12:51:01 PDT)
Re: [AMBER] TI on gpus
(Fri Oct 25 2019 - 06:26:43 PDT)
[AMBER] TI on gpus
(Thu Oct 24 2019 - 10:45:55 PDT)
[AMBER] Thermodynamic integration more questions!
(Wed Oct 23 2019 - 06:50:29 PDT)
Re: [AMBER] Prmtop file creation for thermodynamic integration
(Tue Oct 22 2019 - 13:51:12 PDT)
[AMBER] Prmtop file creation for thermodynamic integration
(Tue Oct 22 2019 - 10:50:56 PDT)
[AMBER] thermodynamic integration parameters in input file
(Tue Oct 22 2019 - 08:44:41 PDT)
[AMBER] TI tutorial for preparation of ligand
(Sun Oct 20 2019 - 09:03:15 PDT)
[AMBER] minimization using restrain weight
(Wed Oct 16 2019 - 06:54:50 PDT)
Re: [AMBER] minimize protein with a small molecule tethered at a fixed location
(Wed Oct 16 2019 - 06:40:42 PDT)
Re: [AMBER] minimize protein with a small molecule tethered at a fixed location
(Wed Oct 16 2019 - 06:32:02 PDT)
[AMBER] minimize protein with a small molecule tethered at a fixed location
(Tue Oct 15 2019 - 16:34:01 PDT)
Re: [AMBER] Thermodynamic integration
(Wed Oct 09 2019 - 11:36:18 PDT)
[AMBER] cpptraj.MPI error
(Mon Oct 07 2019 - 12:33:50 PDT)
Re: [AMBER] Thermodynamic integration
(Thu Oct 03 2019 - 10:48:49 PDT)
Re: [AMBER] Thermodynamic integration
(Thu Oct 03 2019 - 06:41:17 PDT)
[AMBER] Thermodynamic integration
(Tue Oct 01 2019 - 13:25:59 PDT)
diego.soler.uam.es
Re: [AMBER] umbrella sampling question
(Wed Oct 30 2019 - 07:10:23 PDT)
Elvis Martis
Re: [AMBER] Assigning am1-bcc charges to a whole library of ligands
(Sat Oct 26 2019 - 06:39:23 PDT)
Re: [AMBER] REMD Error
(Thu Oct 24 2019 - 22:09:30 PDT)
Re: [AMBER] Problem in extracting pdb file from mdcrd file
(Mon Oct 14 2019 - 01:21:43 PDT)
Re: [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber
(Thu Oct 10 2019 - 08:53:44 PDT)
Re: [AMBER] H - bond tools
(Mon Oct 07 2019 - 23:22:51 PDT)
Faisal Malik
Re: [AMBER] Trouble Installing Amber on Mac
(Fri Oct 11 2019 - 23:35:18 PDT)
[AMBER] Trouble Installing Amber on Mac
(Fri Oct 11 2019 - 21:19:09 PDT)
Fanglue Ni
[AMBER] Amber Installation Problem on Mac
(Thu Oct 03 2019 - 16:35:23 PDT)
Feng Pan
Re: [AMBER] ABMD COM_DISTANCE Help
(Thu Oct 03 2019 - 10:26:37 PDT)
Re: [AMBER] ABMD COM_DISTANCE Help
(Thu Oct 03 2019 - 08:57:51 PDT)
Re: [AMBER] ABMD COM_DISTANCE Help
(Wed Oct 02 2019 - 08:17:04 PDT)
Gerardo Zerbetto De Palma
Re: [AMBER] Gtx 16-series
(Thu Oct 03 2019 - 07:33:28 PDT)
Gert Kruger
Re: [AMBER] Paste command for xleap
(Thu Oct 17 2019 - 23:45:01 PDT)
[AMBER] Paste command for xleap
(Tue Oct 15 2019 - 04:13:28 PDT)
Gustaf Olsson
Re: [AMBER] Some short Catalina experience
(Tue Oct 29 2019 - 06:09:05 PDT)
Re: [AMBER] Some short Catalina experience
(Thu Oct 17 2019 - 23:57:22 PDT)
Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew
(Thu Oct 17 2019 - 12:02:02 PDT)
Re: [AMBER] Check for updates failed
(Thu Oct 17 2019 - 06:25:22 PDT)
Re: [AMBER] Check for updates failed
(Wed Oct 16 2019 - 23:00:32 PDT)
Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew
(Wed Oct 16 2019 - 13:46:00 PDT)
Re: [AMBER] Cataline
(Wed Oct 16 2019 - 13:43:41 PDT)
[AMBER] Check for updates failed
(Wed Oct 16 2019 - 13:21:15 PDT)
Re: [AMBER] Cataline
(Wed Oct 16 2019 - 12:48:34 PDT)
Re: [AMBER] Cataline
(Mon Oct 14 2019 - 13:34:00 PDT)
Re: [AMBER] Cataline
(Sun Oct 13 2019 - 23:48:31 PDT)
[AMBER] Cataline
(Sun Oct 13 2019 - 13:01:37 PDT)
Re: [AMBER] Amber Installation Problem on Mac
(Thu Oct 03 2019 - 23:06:43 PDT)
Re: [AMBER] Rotational/torsion energy
(Thu Oct 03 2019 - 23:01:10 PDT)
Gustavo Seabra
Re: [AMBER] Combining FF14Sb and ForceField_PTM (FF03)... What could possibly go wrong?
(Wed Oct 23 2019 - 17:28:59 PDT)
[AMBER] Combining FF14Sb and ForceField_PTM (FF03)... What could possibly go wrong?
(Wed Oct 23 2019 - 12:21:55 PDT)
Hadi Rahmaninejad
[AMBER] Lennard-Jones parameters in amber and gromacs
(Thu Oct 24 2019 - 08:58:09 PDT)
Hafiz Saqib Ali
[AMBER] Error using MCPB.py
(Mon Oct 07 2019 - 03:58:32 PDT)
Hai Nguyen
Re: [AMBER] make install errors
(Tue Oct 29 2019 - 19:15:06 PDT)
Re: [AMBER] Some short Catalina experience
(Thu Oct 17 2019 - 11:41:13 PDT)
Re: [AMBER] Cataline
(Wed Oct 16 2019 - 13:00:47 PDT)
Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew
(Tue Oct 15 2019 - 08:08:11 PDT)
Re: [AMBER] make install errors
(Mon Oct 14 2019 - 20:27:24 PDT)
Re: [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber
(Fri Oct 11 2019 - 07:32:31 PDT)
Re: [AMBER] "Could not import Amber Python modules!" error
(Wed Oct 09 2019 - 05:59:38 PDT)
Hira Jabeen
Re: [AMBER] NAN error
(Thu Oct 24 2019 - 03:56:06 PDT)
Re: [AMBER] NAN error
(Mon Oct 21 2019 - 09:41:44 PDT)
Re: [AMBER] NAN error
(Mon Oct 21 2019 - 07:14:14 PDT)
Re: [AMBER] NAN error
(Mon Oct 21 2019 - 06:33:56 PDT)
[AMBER] NAN error
(Mon Oct 21 2019 - 06:13:32 PDT)
[AMBER] Imaging issue
(Tue Oct 08 2019 - 03:58:06 PDT)
HOCHEOL LIM
[AMBER] About STOP PMEMD Terminated Abnormally!
(Sat Oct 05 2019 - 02:33:19 PDT)
[AMBER] ERROR: NaNs found in input coordinates.
(Wed Oct 02 2019 - 17:13:05 PDT)
Homeo Morphism
[AMBER] if the ligand doesn't bind when it should, what does it say about quality of my simulations and what can I do?
(Tue Oct 29 2019 - 07:10:49 PDT)
[AMBER] constraining ligands to some distance from a target molecule on pmemd.cuda
(Tue Oct 22 2019 - 13:11:36 PDT)
Jan Brezovsky
[AMBER] Post-doc position in molecular simulations and structural bioinformatics
(Mon Oct 21 2019 - 02:35:18 PDT)
jinfeng liu
[AMBER] How to obtain the pressure in NVT ensemble
(Mon Oct 21 2019 - 23:37:09 PDT)
Jiri Sponer
Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop
(Fri Oct 04 2019 - 00:55:12 PDT)
Junmei Wang
Re: [AMBER] Gaff v2.1 Force Field for n4
(Wed Oct 09 2019 - 10:51:22 PDT)
Kyle Ghaby
Re: [AMBER] ABMD COM_DISTANCE Help
(Thu Oct 03 2019 - 09:17:04 PDT)
Re: [AMBER] ABMD COM_DISTANCE Help
(Wed Oct 02 2019 - 08:41:12 PDT)
[AMBER] ABMD COM_DISTANCE Help
(Tue Oct 01 2019 - 14:16:37 PDT)
Liao
Re: [AMBER] Assigning am1-bcc charges to a whole library of ligands
(Sun Oct 27 2019 - 22:55:21 PDT)
[AMBER] Assigning am1-bcc charges to a whole library of ligands
(Sat Oct 26 2019 - 06:31:56 PDT)
Re: [AMBER] seek help for mmpbsa
(Wed Oct 02 2019 - 04:47:52 PDT)
Lucas Bandeira
Re: [AMBER] Error adding OH⁻ ions in a simulation box
(Tue Oct 22 2019 - 14:09:50 PDT)
[AMBER] Error adding OH⁻ ions in a simulation box
(Mon Oct 21 2019 - 13:44:54 PDT)
Re: [AMBER] Adding OH- to a water box
(Fri Oct 18 2019 - 10:53:06 PDT)
Re: [AMBER] Adding OH- to a water box
(Sun Oct 13 2019 - 10:50:48 PDT)
Re: [AMBER] Adding OH⁻ in a water box
(Sat Oct 12 2019 - 14:05:44 PDT)
[AMBER] Adding OH⁻ in a water box
(Fri Oct 11 2019 - 10:11:33 PDT)
Margarita I. Bernal-Uruchurtu
[AMBER] More ... problems in compilation: fftw3a | Case2 - Using intel
(Mon Oct 14 2019 - 10:42:36 PDT)
[AMBER] More ... problems in compilation: fftw3a | Case1 - Using GNU
(Mon Oct 14 2019 - 10:12:03 PDT)
[AMBER] Problems in compilation: fftw3.a ??
(Fri Oct 11 2019 - 13:05:19 PDT)
Matias Machado
Re: [AMBER] clustering using distance matrix file only
(Mon Oct 21 2019 - 20:12:09 PDT)
Re: [AMBER] Error adding OH⁻ ions in a simulation box
(Mon Oct 21 2019 - 20:05:17 PDT)
Re: [AMBER] Adding OH- to a water box
(Thu Oct 17 2019 - 06:20:19 PDT)
Re: [AMBER] Query regarding DNA
(Fri Oct 11 2019 - 14:10:47 PDT)
Re: [AMBER] Adding OH⁻ in a water box
(Fri Oct 11 2019 - 13:37:18 PDT)
Re: [AMBER] tleap hangs when tries to read new residue
(Mon Oct 07 2019 - 14:35:45 PDT)
Mijiddorj B
Re: [AMBER] "Could not import Amber Python modules!" error
(Wed Oct 09 2019 - 07:54:22 PDT)
Miroslav Suruzhon
[AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber
(Thu Oct 10 2019 - 08:41:57 PDT)
Mooers, Blaine H.M. (HSC)
Re: [AMBER] Amber Installation Problem on Mac: me too
(Fri Oct 04 2019 - 15:29:15 PDT)
MR. RABINDRANATH PAUL
[AMBER] Regarding GIST analysis
(Tue Oct 22 2019 - 00:11:44 PDT)
MYRIAN TORRES RICO
[AMBER] mmpbsa
(Thu Oct 10 2019 - 01:16:59 PDT)
[AMBER] mmpbsa
(Mon Oct 07 2019 - 08:27:12 PDT)
Nate Guerin
[AMBER] Question about ff14SB and parameter files
(Mon Oct 07 2019 - 17:45:40 PDT)
Parviz Seifpanahi Shabane
Re: [AMBER] I add Ions to the system and they don't show up!!!
(Fri Oct 04 2019 - 09:25:34 PDT)
Re: [AMBER] I add Ions to the system and they don't show up!!!
(Wed Oct 02 2019 - 06:59:22 PDT)
[AMBER] I add Ions to the system and they don't show up!!!
(Tue Oct 01 2019 - 08:34:22 PDT)
Paul Westphälinger
[AMBER] CHARMM-GUI now supports Amber
(Fri Oct 04 2019 - 04:47:48 PDT)
Pengfei Li
Re: [AMBER] Error using MCPB.py
(Mon Oct 07 2019 - 07:16:26 PDT)
Re: [AMBER] hydroxyapatite force field parameters
(Mon Oct 07 2019 - 07:13:38 PDT)
Piotr Fajer
Re: [AMBER] Multiple simulations on one GPU
(Tue Oct 29 2019 - 09:59:54 PDT)
Prithvi Raj Pandey
[AMBER] amber99sb-disp forcefield in Amber
(Tue Oct 08 2019 - 10:25:46 PDT)
Ray Luo
Re: [AMBER] Amber Installation Problem on Mac
(Thu Oct 03 2019 - 16:50:23 PDT)
Rinsha Chk
Re: [AMBER] REMD Error
(Tue Oct 29 2019 - 20:21:23 PDT)
Re: [AMBER] REMD Error
(Mon Oct 28 2019 - 20:57:23 PDT)
Re: [AMBER] REMD Error
(Sun Oct 27 2019 - 20:42:57 PDT)
Re: [AMBER] REMD Error
(Sun Oct 27 2019 - 20:42:42 PDT)
Re: [AMBER] REMD Error
(Sat Oct 26 2019 - 04:10:44 PDT)
Re: [AMBER] REMD Error
(Fri Oct 25 2019 - 20:34:01 PDT)
Re: [AMBER] REMD Error
(Thu Oct 24 2019 - 22:19:55 PDT)
[AMBER] REMD Error
(Thu Oct 24 2019 - 21:23:26 PDT)
RITUPARNA ROY
[AMBER] Generating the parameters of a peptide sequence consisting of non-standard amino-acid
(Thu Oct 10 2019 - 08:37:12 PDT)
Robert Molt
[AMBER] Problem in Leap PDB Reading
(Wed Oct 23 2019 - 19:13:41 PDT)
Rosellen, Martin
Re: [AMBER] Calculate MMGBSA keeping water in binding site
(Mon Oct 21 2019 - 04:39:17 PDT)
Re: [AMBER] Calculate MMGBSA keeping water in binding site
(Sat Oct 05 2019 - 06:40:18 PDT)
[AMBER] Calculate MMGBSA keeping water in binding site
(Fri Oct 04 2019 - 06:27:27 PDT)
Ross Walker
Re: [AMBER] TI on gpus
(Thu Oct 24 2019 - 17:56:06 PDT)
Re: [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ?
(Sun Oct 06 2019 - 13:22:33 PDT)
Rui Chen
[AMBER] PTRAJ (clustering)-Segmentation fault
(Tue Oct 15 2019 - 08:35:56 PDT)
Re: [AMBER] CPPTRAJ parameter file error
(Thu Oct 10 2019 - 15:49:43 PDT)
Re: [AMBER] CPPTRAJ parameter file error
(Wed Oct 09 2019 - 15:41:30 PDT)
Re: [AMBER] CPPTRAJ parameter file error
(Mon Oct 07 2019 - 21:27:20 PDT)
Re: [AMBER] CPPTRAJ parameter file error
(Fri Oct 04 2019 - 10:31:35 PDT)
Re: [AMBER] CPPTRAJ parameter file error
(Wed Oct 02 2019 - 15:18:04 PDT)
Re: [AMBER] CPPTRAJ parameter file error
(Wed Oct 02 2019 - 07:41:54 PDT)
[AMBER] CPPTRAJ parameter file error
(Tue Oct 01 2019 - 15:36:19 PDT)
Ryoichi Utsumi
Re: [AMBER] Installaiton of pmemd for Amber16
(Mon Sep 30 2019 - 19:31:35 PDT)
Sadaf Rani
[AMBER] strip problem in cpptraj
(Fri Oct 25 2019 - 10:58:30 PDT)
Re: [AMBER] Prmtop file creation for thermodynamic integration
(Tue Oct 22 2019 - 11:07:42 PDT)
[AMBER] free energy calculation and leap error
(Tue Oct 22 2019 - 09:03:04 PDT)
Re: [AMBER] Thermodynamic integration
(Thu Oct 17 2019 - 04:19:01 PDT)
Re: [AMBER] Thermodynamic integration
(Mon Oct 14 2019 - 12:02:52 PDT)
Re: [AMBER] Thermodynamic integration
(Mon Oct 14 2019 - 08:10:46 PDT)
Re: [AMBER] Thermodynamic integration
(Mon Oct 14 2019 - 03:59:22 PDT)
Re: [AMBER] Thermodynamic integration
(Thu Oct 10 2019 - 07:45:13 PDT)
Re: [AMBER] Thermodynamic integration
(Thu Oct 10 2019 - 05:16:31 PDT)
Re: [AMBER] Thermodynamic integration
(Thu Oct 03 2019 - 08:06:17 PDT)
Saikat Pal
[AMBER] Query regarding DNA
(Fri Oct 11 2019 - 08:21:20 PDT)
Sarath Dantu (Staff)
[AMBER] netcdf: issue with timestamp
(Tue Oct 01 2019 - 06:26:27 PDT)
Schröder, David Christopher
Re: [AMBER] error while running pmemd.cuda after reinstallation of amber 16
(Wed Oct 23 2019 - 09:16:42 PDT)
[AMBER] error while running pmemd.cuda after reinstallation of amber 16
(Tue Oct 22 2019 - 01:36:16 PDT)
Scott Brozell
Re: [AMBER] sander/lmod parallel execution
(Mon Oct 21 2019 - 11:20:49 PDT)
Re: [AMBER] Some short Catalina experience
(Thu Oct 17 2019 - 11:02:02 PDT)
Seketoulie Keretsu
[AMBER] MMPBSA.py resulted in DELTA TOTAL= 1414 kcal/mole
(Sun Oct 13 2019 - 16:55:20 PDT)
[AMBER] regarding amber licensed version and free version.
(Tue Oct 01 2019 - 09:06:48 PDT)
Shayna Hilburg
Re: [AMBER] atomicfluct/rmsf time
(Sat Oct 26 2019 - 16:18:39 PDT)
[AMBER] atomicfluct/rmsf time
(Fri Oct 25 2019 - 13:40:45 PDT)
shivangi agarwal
Re: [AMBER] H - bond tools
(Sat Oct 12 2019 - 22:08:11 PDT)
Re: [AMBER] H - bond tools
(Mon Oct 07 2019 - 23:31:05 PDT)
[AMBER] H - bond tools
(Mon Oct 07 2019 - 23:10:05 PDT)
Sodiq Waheed
[AMBER] Error in Step two of MCPB
(Wed Oct 30 2019 - 05:15:04 PDT)
Steven Ramsey
Re: [AMBER] Regarding GIST analysis
(Tue Oct 22 2019 - 08:23:47 PDT)
Sudad Dayl
[AMBER] MD simulation system
(Sat Oct 26 2019 - 07:26:36 PDT)
Sunita Patel
Re: [AMBER] Error during the test of amber 18 installation
(Thu Oct 10 2019 - 22:43:42 PDT)
[AMBER] Error during the test of amber 18 installation
(Wed Oct 09 2019 - 04:33:53 PDT)
Re: [AMBER] Error during the test of amber 18 installation
(Mon Oct 07 2019 - 04:30:33 PDT)
Re: [AMBER] Error during the test of amber 18 installation
(Fri Oct 04 2019 - 00:10:00 PDT)
[AMBER] Error during the test of amber 18 installation
(Wed Oct 02 2019 - 07:18:35 PDT)
Re: [AMBER] Amber18 installation
(Mon Sep 30 2019 - 22:14:43 PDT)
sunyeping
Re: [AMBER] "Could not import Amber Python modules!" error
(Fri Oct 11 2019 - 03:55:21 PDT)
Re: [AMBER] "Could not import Amber Python modules!" error
(Wed Oct 09 2019 - 07:43:49 PDT)
[AMBER] "Could not import Amber Python modules!" error
(Wed Oct 09 2019 - 05:28:52 PDT)
Supriyo Bhattacharya
Re: [AMBER] amber99sb-disp forcefield in Amber
(Tue Oct 08 2019 - 12:02:51 PDT)
Suruzhon M.
Re: [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber
(Fri Oct 11 2019 - 07:31:11 PDT)
Swagata Halder
Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop
(Thu Oct 03 2019 - 23:20:45 PDT)
[AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop
(Thu Oct 03 2019 - 00:58:58 PDT)
Swantje Mohr
[AMBER] compiling with -noX11 option
(Tue Oct 22 2019 - 11:22:16 PDT)
Tal Duanias
Re: [AMBER] hydroxyapatite force field parameters
(Mon Oct 07 2019 - 10:09:23 PDT)
[AMBER] hydroxyapatite force field parameters
(Mon Oct 07 2019 - 00:20:47 PDT)
Thomas Cheatham
Re: [AMBER] PTRAJ (clustering)-Segmentation fault
(Tue Oct 15 2019 - 13:11:10 PDT)
Tim Davis
Re: [AMBER] clustering using distance matrix file only
(Tue Oct 22 2019 - 14:09:54 PDT)
[AMBER] clustering using distance matrix file only
(Sat Oct 19 2019 - 15:26:51 PDT)
Tru Huynh
Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew
(Thu Oct 17 2019 - 08:36:36 PDT)
[AMBER] (long) OSX/catalina Ambertools19 building success with brew
(Tue Oct 15 2019 - 03:05:31 PDT)
Venkata Krishnan Ramaswamy
[AMBER] symmetry corrected rms fitting
(Mon Oct 14 2019 - 06:30:56 PDT)
Vlad Cojocaru
[AMBER] compiling Amber with gcc 9.2 and intel mpi 2019
(Mon Oct 28 2019 - 07:57:51 PDT)
[AMBER] restraining a peptide to devoid of any secondary structure
(Wed Oct 02 2019 - 07:11:06 PDT)
Wesley Michael Botello-Smith
Re: [AMBER] if the ligand doesn't bind when it should, what does it say about quality of my simulations and what can I do?
(Tue Oct 29 2019 - 14:37:07 PDT)
xmgign.126.com
[AMBER] Is it necessary to set "baroscalingdir" in the membrane system?
(Fri Oct 11 2019 - 01:29:06 PDT)
Yang JIANG
[AMBER] How to check the convergence of NEB calculation?
(Fri Oct 25 2019 - 15:19:09 PDT)
Zhendong Li
Re: [AMBER] DNA methylation parameters
(Tue Oct 01 2019 - 07:50:20 PDT)
Åsmund Røhr Kjendseth
Re: [AMBER] ff19SB update
(Thu Oct 17 2019 - 23:47:44 PDT)
[AMBER] ff19SB update
(Wed Oct 16 2019 - 06:10:05 PDT)
崔佳文
[AMBER] Problem in MMPBSA analysis
(Tue Oct 08 2019 - 19:39:30 PDT)
杨明俊
Re: [AMBER] more efficient TI rerun over existing trajectory
(Mon Oct 28 2019 - 06:12:56 PDT)
Re: [AMBER] more efficient TI rerun over existing trajectory
(Thu Oct 17 2019 - 06:35:27 PDT)
[AMBER] more efficient TI rerun over existing trajectory
(Wed Oct 16 2019 - 20:25:04 PDT)
石娜
[AMBER] seek help for mmpbsa
(Wed Oct 02 2019 - 03:42:48 PDT)
邸春艳
[AMBER] About the unit of the pressure in the md.out file?
(Mon Oct 28 2019 - 00:35:14 PDT)
钟海洋
[AMBER] tip4pew water module in different version performs different
(Thu Oct 31 2019 - 01:54:42 PDT)
Re: [AMBER] umbrella sampling question
(Wed Oct 30 2019 - 20:45:42 PDT)
[AMBER] umbrella sampling question
(Tue Oct 29 2019 - 23:59:38 PDT)
조준범
[AMBER] Problem with installation of AMBER
(Mon Oct 21 2019 - 02:56:02 PDT)
[AMBER] Problem with Installation of AMBER
(Sat Oct 19 2019 - 08:02:01 PDT)
[AMBER] How can I use modified GAFF?
(Mon Oct 07 2019 - 00:40:13 PDT)
Last message date
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Thu Oct 31 2019 - 06:00:02 PDT
Archived on
: Mon Nov 25 2024 - 05:55:46 PST
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