Amber Archive Jun 2017 by author
508 messages
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Starting
Wed May 31 2017 - 19:30:02 PDT,
Ending
Fri Jun 30 2017 - 23:00:03 PDT
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Abhilash J
Re: [AMBER] A conceptual question on MMGBSA binding and RMSF analysis
(Wed Jun 14 2017 - 09:08:31 PDT)
[AMBER] A conceptual question on MMGBSA binding and RMSF analysis
(Wed Jun 14 2017 - 04:42:23 PDT)
Adrian Roitberg
Re: [AMBER] TI/FEP on GPU in Amber?
(Fri Jun 30 2017 - 09:17:24 PDT)
Re: [AMBER] constant pH MD question
(Thu Jun 29 2017 - 07:39:32 PDT)
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Tue Jun 20 2017 - 13:30:00 PDT)
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Tue Jun 20 2017 - 12:38:41 PDT)
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Tue Jun 20 2017 - 11:45:43 PDT)
Re: [AMBER] relaxation time to maintain quasi-static condition
(Tue Jun 20 2017 - 11:29:56 PDT)
Re: [AMBER] relaxation time to maintain quasi-static condition
(Tue Jun 20 2017 - 05:48:05 PDT)
Re: [AMBER] PCA analysis
(Thu Jun 08 2017 - 09:55:54 PDT)
Re: [AMBER] Poor performance of REMD simulation
(Wed Jun 07 2017 - 13:58:02 PDT)
Re: [AMBER] Velocity autocorrelation
(Wed Jun 07 2017 - 09:41:54 PDT)
Alessandro Contini
Re: [AMBER] issue in antechamber17 bcc charges with mopac
(Wed Jun 21 2017 - 07:04:11 PDT)
[AMBER] issue in antechamber17 bcc charges with mopac
(Wed Jun 21 2017 - 04:48:17 PDT)
Alexander Martin Spring-Connell
Re: [AMBER] LEAP Merging Atom Types
(Tue Jun 20 2017 - 15:40:06 PDT)
Re: [AMBER] LEAP Merging Atom Types
(Tue Jun 20 2017 - 15:14:09 PDT)
Re: [AMBER] Issue installing Amber16 cuda
(Fri Jun 16 2017 - 08:49:09 PDT)
[AMBER] Issue installing Amber16 cuda
(Fri Jun 16 2017 - 05:05:38 PDT)
Andreas Tosstorff
[AMBER] Parametrization of a phosphorylated small molecule
(Thu Jun 29 2017 - 05:31:54 PDT)
[AMBER] Question about ergodicity and MD
(Wed Jun 21 2017 - 02:09:34 PDT)
[AMBER] ERROR: nfft1 must be in the range of 6 to 512!
(Thu Jun 08 2017 - 05:38:36 PDT)
Re: [AMBER] pmemd: posixio...failed
(Thu Jun 08 2017 - 05:31:04 PDT)
[AMBER] pmemd: posixio...failed
(Tue Jun 06 2017 - 09:49:26 PDT)
Andrew Schaub
Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440
(Thu Jun 29 2017 - 23:35:55 PDT)
Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440
(Thu Jun 29 2017 - 21:31:46 PDT)
Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440
(Thu Jun 29 2017 - 21:30:00 PDT)
Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440
(Thu Jun 29 2017 - 20:18:45 PDT)
Re: [AMBER] constant pH MD question
(Thu Jun 29 2017 - 06:46:47 PDT)
Re: [AMBER] Heme parameter error
(Wed Jun 28 2017 - 21:19:36 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Wed Jun 28 2017 - 21:16:13 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 20:55:52 PDT)
Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB
(Wed Jun 21 2017 - 09:35:46 PDT)
Arati Paudyal
Re: [AMBER] mbondi set up
(Sun Jun 25 2017 - 05:22:07 PDT)
Ashish Radadiya
Re: [AMBER] How to solve the unfilled valence problem in antechamber
(Fri Jun 16 2017 - 11:17:58 PDT)
Re: [AMBER] How to solve the unfilled valence problem in antechamber
(Fri Jun 16 2017 - 02:41:58 PDT)
Re: [AMBER] How to solve the unfilled valence problem in antechamber
(Thu Jun 15 2017 - 06:23:31 PDT)
ATUL KUMAR
Re: [AMBER] Velocity autocorrelation
(Wed Jun 07 2017 - 09:37:46 PDT)
[AMBER] Velocity autocorrelation
(Wed Jun 07 2017 - 04:22:37 PDT)
Ayesha Fatima
[AMBER] error in qmmm
(Sat Jun 03 2017 - 06:58:44 PDT)
Baker, Joseph
Re: [AMBER] using mmgbsa for dna/protein
(Tue Jun 27 2017 - 20:41:29 PDT)
[AMBER] using mmgbsa for dna/protein
(Tue Jun 27 2017 - 20:18:11 PDT)
Re: [AMBER] mmpbsa
(Mon Jun 26 2017 - 18:15:09 PDT)
[AMBER] mmpbsa
(Mon Jun 26 2017 - 14:50:30 PDT)
Bala subramanian
[AMBER] correlated dihedrals in ff parameterization
(Thu Jun 22 2017 - 01:42:58 PDT)
Bill Ross
Re: [AMBER] problem in setting AMBERHOME environment variable using cygwin
(Fri Jun 30 2017 - 14:10:37 PDT)
Re: [AMBER] problem in setting AMBERHOME environment variable using cygwin
(Fri Jun 30 2017 - 10:38:57 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Thu Jun 29 2017 - 13:20:50 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 23:52:38 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 23:19:58 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 22:59:06 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 21:57:52 PDT)
Re: [AMBER] TI free energy calculation errors
(Wed Jun 28 2017 - 12:58:33 PDT)
Re: [AMBER] TI free energy calculation errors
(Wed Jun 28 2017 - 12:51:35 PDT)
Re: [AMBER] TI free energy calculation errors
(Wed Jun 28 2017 - 12:43:20 PDT)
Re: [AMBER] TI free energy calculation errors
(Wed Jun 28 2017 - 12:08:37 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 11:21:56 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 11:08:09 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 10:55:58 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 10:46:40 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 10:44:27 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 10:34:36 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 10:27:11 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Tue Jun 27 2017 - 23:50:01 PDT)
Re: [AMBER] LEAP Merging Atom Types
(Wed Jun 21 2017 - 09:19:28 PDT)
Re: [AMBER] "Abort trap 6" error message with tLeap and xLeap
(Wed Jun 21 2017 - 04:54:09 PDT)
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Tue Jun 20 2017 - 16:41:56 PDT)
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Tue Jun 20 2017 - 13:57:37 PDT)
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Tue Jun 20 2017 - 13:55:08 PDT)
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Tue Jun 20 2017 - 13:51:50 PDT)
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Tue Jun 20 2017 - 13:50:18 PDT)
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Tue Jun 20 2017 - 12:34:45 PDT)
Re: [AMBER] NFE dihedral
(Sun Jun 18 2017 - 15:16:13 PDT)
Re: [AMBER] Warning during minimization
(Thu Jun 15 2017 - 21:27:40 PDT)
Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB
(Thu Jun 15 2017 - 01:33:48 PDT)
Re: [AMBER] Warning during minimization
(Wed Jun 14 2017 - 23:20:52 PDT)
Re: [AMBER] Warning during minimization
(Wed Jun 14 2017 - 18:30:49 PDT)
Re: [AMBER] Warning during minimization
(Wed Jun 14 2017 - 18:20:07 PDT)
Re: [AMBER] Fwd: test serial amber 14 and ambertool15
(Wed Jun 14 2017 - 10:55:43 PDT)
Re: [AMBER] Problem in creating topology and coordinate files
(Sat Jun 10 2017 - 22:53:34 PDT)
Re: [AMBER] Is explicit solvent more accurate than implicit solvent?
(Wed Jun 07 2017 - 01:09:55 PDT)
Re: [AMBER] External electric fields support for GPU and how to set the parameters in mdin files?
(Wed Jun 07 2017 - 00:02:03 PDT)
Re: [AMBER] Questions about special periodic boundary conditions.
(Thu Jun 01 2017 - 10:11:21 PDT)
Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial
(Thu Jun 01 2017 - 10:09:24 PDT)
Billy Williams-Noonan
Re: [AMBER] MD simulation of the whole protein or just its ligand-binding domain
(Tue Jun 06 2017 - 02:39:39 PDT)
Brent Krueger
Re: [AMBER] Weighting factors in multi conformational resp fitting
(Tue Jun 06 2017 - 04:57:49 PDT)
Carlos Simmerling
Re: [AMBER] Free energy path
(Fri Jun 23 2017 - 06:45:03 PDT)
Re: [AMBER] Weired behaviour during Heating
(Fri Jun 16 2017 - 11:41:46 PDT)
Re: [AMBER] Weired behaviour during Heating
(Fri Jun 16 2017 - 07:31:52 PDT)
Re: [AMBER] RMSD
(Mon Jun 05 2017 - 14:20:51 PDT)
carmine marco morgillo
[AMBER] TI in dimeric enzyme
(Wed Jun 07 2017 - 09:44:00 PDT)
Charles Lin
Re: [AMBER] External electric fields support for GPU and how to set the parameters in mdin files?
(Tue Jun 06 2017 - 23:21:35 PDT)
Re: [AMBER] external electric field in Amber 16
(Wed May 31 2017 - 19:02:47 PDT)
Charles-Alexandre Mattelaer
Re: [AMBER] mdgx extracting energies
(Wed Jun 14 2017 - 07:56:14 PDT)
[AMBER] mdgx extracting energies
(Mon Jun 12 2017 - 06:36:27 PDT)
Chris Moth
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Wed Jun 21 2017 - 14:37:43 PDT)
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Tue Jun 20 2017 - 12:27:08 PDT)
[AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Tue Jun 20 2017 - 11:29:41 PDT)
Re: [AMBER] inpcrd file format in AmberTools16
(Tue Jun 13 2017 - 09:55:59 PDT)
Re: [AMBER] No Torsion terms
(Thu Jun 01 2017 - 08:46:19 PDT)
Chris Neale
Re: [AMBER] set substrate concentration gradient difference acorss membrane
(Mon Jun 05 2017 - 20:29:05 PDT)
co nguyentruong
Re: [AMBER] Fwd: test serial amber 14 and ambertool15
(Wed Jun 14 2017 - 16:02:52 PDT)
Re: [AMBER] Fwd: test serial amber 14 and ambertool15
(Wed Jun 14 2017 - 15:55:11 PDT)
[AMBER] Fwd: test serial amber 14 and ambertool15
(Wed Jun 14 2017 - 07:58:38 PDT)
Daniel Roe
Re: [AMBER] Mm_pbsa.pl using netcdf trajectory
(Fri Jun 30 2017 - 07:49:11 PDT)
Re: [AMBER] ambpdb- Segmentation fault (core dumped)
(Wed Jun 28 2017 - 08:22:53 PDT)
Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time
(Wed Jun 28 2017 - 05:45:56 PDT)
Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time
(Mon Jun 26 2017 - 09:06:15 PDT)
Re: [AMBER] Download and installing cpptraj sub-application
(Mon Jun 26 2017 - 05:55:34 PDT)
Re: [AMBER] error running mmpbsa
(Mon Jun 26 2017 - 05:54:47 PDT)
Re: [AMBER] AMber trajectory to Gromacs trajectory
(Mon Jun 26 2017 - 05:50:20 PDT)
Re: [AMBER] AMber trajectory to Gromacs trajectory
(Sat Jun 24 2017 - 04:57:32 PDT)
Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time
(Thu Jun 22 2017 - 12:52:24 PDT)
Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time
(Thu Jun 22 2017 - 08:55:07 PDT)
Re: [AMBER] " possible FAILURE " messages
(Wed Jun 21 2017 - 06:42:59 PDT)
Re: [AMBER] Hydrogen bond Average distance
(Wed Jun 21 2017 - 06:23:31 PDT)
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Wed Jun 21 2017 - 05:42:11 PDT)
Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes
(Wed Jun 21 2017 - 05:38:03 PDT)
Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes
(Wed Jun 21 2017 - 05:33:18 PDT)
Re: [AMBER] convert .nc trajectories to .xyz
(Mon Jun 19 2017 - 11:10:58 PDT)
Re: [AMBER] Formula/reference for ambertools native contact calculations
(Mon Jun 12 2017 - 10:02:35 PDT)
Re: [AMBER] Center of mass
(Wed Jun 07 2017 - 09:33:16 PDT)
Re: [AMBER] Is explicit solvent more accurate than implicit solvent?
(Wed Jun 07 2017 - 06:52:09 PDT)
Re: [AMBER] Center of mass
(Wed Jun 07 2017 - 06:39:33 PDT)
Re: [AMBER] Velocity autocorrelation
(Wed Jun 07 2017 - 06:35:43 PDT)
Re: [AMBER] pmemd: posixio...failed
(Tue Jun 06 2017 - 10:14:30 PDT)
Re: [AMBER] Center of mass
(Tue Jun 06 2017 - 08:59:22 PDT)
Re: [AMBER] RMSD
(Tue Jun 06 2017 - 08:07:09 PDT)
Re: [AMBER] average no. of H bond between ligand-solvent.
(Tue Jun 06 2017 - 05:25:56 PDT)
Re: [AMBER] cuda vs. mpi vs. mpi-cuda
(Mon Jun 05 2017 - 05:15:31 PDT)
Re: [AMBER] center of mass of Guanine
(Fri Jun 02 2017 - 06:33:36 PDT)
Re: [AMBER] Error during the installion
(Thu Jun 01 2017 - 06:05:01 PDT)
Re: [AMBER] Error during the installion
(Thu Jun 01 2017 - 05:44:52 PDT)
David A Case
Re: [AMBER] problem in setting AMBERHOME environment variable using cygwin
(Fri Jun 30 2017 - 14:08:33 PDT)
Re: [AMBER] Parametrization of a phosphorylated small molecule
(Fri Jun 30 2017 - 11:16:26 PDT)
Re: [AMBER] problem of installing amber17 in window 10 using cygwin
(Fri Jun 30 2017 - 11:02:59 PDT)
Re: [AMBER] Amber md in HPC : Job terminated
(Thu Jun 22 2017 - 05:17:46 PDT)
Re: [AMBER] Free energy path
(Wed Jun 21 2017 - 06:02:39 PDT)
Re: [AMBER] issue in antechamber17 bcc charges with mopac
(Wed Jun 21 2017 - 05:57:37 PDT)
Re: [AMBER] "Abort trap 6" error message with tLeap and xLeap
(Wed Jun 21 2017 - 05:45:24 PDT)
Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes
(Wed Jun 21 2017 - 05:34:49 PDT)
Re: [AMBER] LEAP Merging Atom Types
(Wed Jun 21 2017 - 05:27:24 PDT)
Re: [AMBER] Regarding empty lig.frcmod file
(Fri Jun 09 2017 - 05:56:23 PDT)
Re: [AMBER] SASA calculation
(Fri Jun 09 2017 - 05:49:26 PDT)
Re: [AMBER] ERROR: nfft1 must be in the range of 6 to 512!
(Thu Jun 08 2017 - 08:15:55 PDT)
Re: [AMBER] Normal mode entropy calculations for active site residues
(Thu Jun 08 2017 - 05:40:34 PDT)
Re: [AMBER] cuda vs. mpi vs. mpi-cuda
(Mon Jun 05 2017 - 05:17:57 PDT)
Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial
(Thu Jun 01 2017 - 12:23:22 PDT)
Re: [AMBER] Error during the installion
(Thu Jun 01 2017 - 06:34:02 PDT)
Re: [AMBER] external electric field in Amber 16
(Thu Jun 01 2017 - 06:16:12 PDT)
David Case
Re: [AMBER] Is there any analysis of the stability of DNA in presence of Divalent cation??
(Thu Jun 29 2017 - 10:09:04 PDT)
Re: [AMBER] AMBER Digest, Vol 1973, Issue 1
(Thu Jun 29 2017 - 07:35:50 PDT)
Re: [AMBER] antechamber
(Thu Jun 29 2017 - 07:27:57 PDT)
Re: [AMBER] Parabolic restraint with nmropt
(Tue Jun 27 2017 - 08:17:56 PDT)
Re: [AMBER] Problem of running ANTECHAMBER
(Sat Jun 24 2017 - 05:46:22 PDT)
Re: [AMBER] LEAP Merging Atom Types
(Fri Jun 23 2017 - 07:57:13 PDT)
Re: [AMBER] Leap: Periodic Boundary of DNA
(Wed Jun 21 2017 - 17:52:43 PDT)
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Tue Jun 20 2017 - 13:20:28 PDT)
Re: [AMBER] relaxation time to maintain quasi-static condition
(Tue Jun 20 2017 - 05:28:24 PDT)
Re: [AMBER] How to solve the unfilled valence problem in antechamber
(Sun Jun 18 2017 - 11:51:09 PDT)
Re: [AMBER] Regarding empty lig.frcmod file
(Fri Jun 16 2017 - 08:08:38 PDT)
Re: [AMBER] Issue installing Amber16 cuda
(Fri Jun 16 2017 - 08:00:38 PDT)
Re: [AMBER] How to solve the unfilled valence problem in antechamber
(Fri Jun 16 2017 - 07:54:59 PDT)
Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB
(Fri Jun 16 2017 - 07:53:10 PDT)
Re: [AMBER] Weired behaviour during Heating
(Fri Jun 16 2017 - 07:26:39 PDT)
Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB
(Thu Jun 15 2017 - 12:34:28 PDT)
Re: [AMBER] How to solve the unfilled valence problem in antechamber
(Thu Jun 15 2017 - 12:29:58 PDT)
Re: [AMBER] Fwd: test serial amber 14 and ambertool15
(Thu Jun 15 2017 - 08:13:12 PDT)
Re: [AMBER] A conceptual question on MMGBSA binding and RMSF analysis
(Thu Jun 15 2017 - 08:08:19 PDT)
Re: [AMBER] Warning during minimization
(Thu Jun 15 2017 - 08:01:43 PDT)
Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB
(Thu Jun 15 2017 - 07:24:14 PDT)
Re: [AMBER] Neutral N-terminal proline parameter in AMBER force field
(Tue Jun 13 2017 - 07:00:37 PDT)
Re: [AMBER] inpcrd file format in AmberTools16
(Mon Jun 12 2017 - 17:28:14 PDT)
Re: [AMBER] RNA parameters for wc_helix
(Mon Jun 12 2017 - 17:12:47 PDT)
Re: [AMBER] Fwd: SASA calculation
(Mon Jun 12 2017 - 04:41:43 PDT)
Re: [AMBER] RNA parameters for wc_helix
(Mon Jun 12 2017 - 04:38:53 PDT)
Re: [AMBER] Problem in creating topology and coordinate files
(Sun Jun 11 2017 - 05:06:47 PDT)
Re: [AMBER] Is explicit solvent more accurate than implicit solvent?
(Wed Jun 07 2017 - 18:19:03 PDT)
Re: [AMBER] Calculation of Volume fraction
(Wed Jun 07 2017 - 09:26:53 PDT)
David Cerutti
Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps
(Tue Jun 20 2017 - 11:39:52 PDT)
Re: [AMBER] Specific GPU for running pmemd.cuda
(Fri Jun 16 2017 - 13:08:31 PDT)
Re: [AMBER] mdgx extracting energies
(Mon Jun 12 2017 - 21:46:32 PDT)
Re: [AMBER] mdgx extracting energies
(Mon Jun 12 2017 - 21:23:53 PDT)
Re: [AMBER] cuda vs. mpi vs. mpi-cuda
(Sun Jun 04 2017 - 13:11:13 PDT)
Dd H
Re: [AMBER] Is explicit solvent more accurate than implicit solvent?
(Wed Jun 07 2017 - 19:07:12 PDT)
Re: [AMBER] Is explicit solvent more accurate than implicit solvent?
(Wed Jun 07 2017 - 01:38:00 PDT)
[AMBER] Is explicit solvent more accurate than implicit solvent?
(Wed Jun 07 2017 - 01:06:46 PDT)
Dean Cuebas
Re: [AMBER] Selecting histidine Protonation state for simulation
(Thu Jun 15 2017 - 16:30:36 PDT)
diego.soler.uam.es
Re: [AMBER] Question about ergodicity and MD
(Wed Jun 21 2017 - 04:03:49 PDT)
Re: [AMBER] Is explicit solvent more accurate than implicit solvent?
(Wed Jun 07 2017 - 03:00:14 PDT)
Dr. M. Shahid
Re: [AMBER] Issue installing Amber16 cuda
(Fri Jun 16 2017 - 06:08:17 PDT)
Dr. Robert Molt
[AMBER] inpcrd file format in AmberTools16
(Mon Jun 12 2017 - 10:45:33 PDT)
Eiros Zamora, Juan
Re: [AMBER] Weighting factors in multi conformational resp fitting
(Tue Jun 06 2017 - 07:05:57 PDT)
[AMBER] Weighting factors in multi conformational resp fitting
(Tue Jun 06 2017 - 04:05:16 PDT)
Elisa Pieri
[AMBER] Cluster analysis
(Wed Jun 28 2017 - 08:51:00 PDT)
Elvis Martis
Re: [AMBER] Mm_pbsa.pl using netcdf trajectory
(Fri Jun 30 2017 - 08:22:00 PDT)
[AMBER] Mm_pbsa.pl using netcdf trajectory
(Fri Jun 30 2017 - 01:18:14 PDT)
Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440
(Thu Jun 29 2017 - 21:19:13 PDT)
Re: [AMBER] kindly see the leap.log for fe---02
(Thu Jun 29 2017 - 21:17:02 PDT)
Re: [AMBER] kindly see the leap.log for fe---02
(Thu Jun 29 2017 - 20:58:41 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 23:16:20 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 22:56:13 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 22:52:13 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 21:37:52 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Wed Jun 28 2017 - 21:32:37 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 20:29:04 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Wed Jun 28 2017 - 20:26:31 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Wed Jun 28 2017 - 12:06:18 PDT)
Re: [AMBER] Cluster analysis
(Wed Jun 28 2017 - 09:29:28 PDT)
Re: [AMBER] ambpdb- Segmentation fault (core dumped)
(Wed Jun 28 2017 - 05:46:58 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Tue Jun 27 2017 - 23:57:20 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Tue Jun 27 2017 - 22:36:28 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Tue Jun 27 2017 - 21:27:59 PDT)
Re: [AMBER] error running mmpbsa
(Tue Jun 27 2017 - 21:25:49 PDT)
Re: [AMBER] how heme force field combine with amber 99 ff
(Tue Jun 27 2017 - 00:03:08 PDT)
Re: [AMBER] how heme force field combine with amber 99 ff
(Mon Jun 26 2017 - 18:24:08 PDT)
Re: [AMBER] error running mmpbsa
(Mon Jun 26 2017 - 18:18:13 PDT)
Re: [AMBER] mbondi set up
(Sun Jun 25 2017 - 05:18:36 PDT)
Re: [AMBER] error running mmpbsa
(Sat Jun 24 2017 - 20:35:48 PDT)
Re: [AMBER] Download and installing cpptraj sub-application
(Sat Jun 24 2017 - 04:06:00 PDT)
Re: [AMBER] Problem of running ANTECHAMBER
(Fri Jun 23 2017 - 22:18:53 PDT)
Re: [AMBER] problem in creating topology and coordinate files
(Fri Jun 23 2017 - 22:17:40 PDT)
Re: [AMBER] error running mmpbsa
(Fri Jun 23 2017 - 20:43:49 PDT)
Re: [AMBER] error running mmpbsa
(Fri Jun 23 2017 - 18:09:56 PDT)
Re: [AMBER] Amber md in HPC : Job terminated
(Thu Jun 22 2017 - 04:35:59 PDT)
Re: [AMBER] Regarding empty lig.frcmod file
(Fri Jun 16 2017 - 02:16:18 PDT)
Re: [AMBER] Regarding empty lig.frcmod file
(Thu Jun 15 2017 - 23:55:20 PDT)
Re: [AMBER] Fwd: test serial amber 14 and ambertool15
(Wed Jun 14 2017 - 08:27:44 PDT)
Re: [AMBER] A conceptual question on MMGBSA binding and RMSF analysis
(Wed Jun 14 2017 - 08:25:15 PDT)
Re: [AMBER] convert .nc trajectories to .xyz
(Wed Jun 14 2017 - 02:39:34 PDT)
Re: [AMBER] Fwd: SASA calculation
(Mon Jun 12 2017 - 00:17:05 PDT)
Re: [AMBER] Split trajectory
(Sun Jun 11 2017 - 05:48:31 PDT)
Re: [AMBER] Regarding empty lig.frcmod file
(Fri Jun 09 2017 - 06:06:38 PDT)
Re: [AMBER] Regarding empty lig.frcmod file
(Fri Jun 09 2017 - 05:29:36 PDT)
Re: [AMBER] Regarding empty lig.frcmod file
(Fri Jun 09 2017 - 04:30:34 PDT)
Re: [AMBER] SASA calculation
(Fri Jun 09 2017 - 00:04:07 PDT)
Re: [AMBER] visualizing first mode of motion from PCA analysis in chimera or vmd
(Thu Jun 08 2017 - 21:46:55 PDT)
Re: [AMBER] PCA analysis
(Thu Jun 08 2017 - 21:45:58 PDT)
Re: [AMBER] Normal mode entropy calculations for active site residues
(Tue Jun 06 2017 - 21:18:05 PDT)
Re: [AMBER] Regarding empty lig.frcmod file
(Tue Jun 06 2017 - 09:32:04 PDT)
Re: [AMBER] average no. of H bond between ligand-solvent.
(Tue Jun 06 2017 - 05:16:56 PDT)
Re: [AMBER] AMBER Digest, Vol 1932, Issue 1
(Tue Jun 06 2017 - 02:43:21 PDT)
Eugene Cha
[AMBER] MCPB step 2 local variable 'ban' referenced before assignment
(Wed Jun 28 2017 - 23:15:55 PDT)
[AMBER] SN is required in naa_mol2files but not provided
(Mon Jun 26 2017 - 06:04:14 PDT)
Fabrício Bracht
Re: [AMBER] NFE dihedral
(Sun Jun 18 2017 - 13:47:57 PDT)
Re: [AMBER] NFE dihedral
(Fri Jun 16 2017 - 16:05:13 PDT)
Re: [AMBER] NFE dihedral
(Wed Jun 14 2017 - 11:36:49 PDT)
Re: [AMBER] NFE dihedral
(Wed Jun 14 2017 - 08:47:01 PDT)
[AMBER] NFE dihedral
(Tue Jun 13 2017 - 13:55:15 PDT)
Feng Pan
Re: [AMBER] NFE dihedral
(Sun Jun 18 2017 - 19:14:26 PDT)
Re: [AMBER] NFE dihedral
(Fri Jun 16 2017 - 16:41:19 PDT)
Re: [AMBER] NFE dihedral
(Wed Jun 14 2017 - 10:13:23 PDT)
Re: [AMBER] NFE dihedral
(Tue Jun 13 2017 - 14:48:43 PDT)
Gabriel Jara
Re: [AMBER] AMBER Digest, Vol 1951, Issue 1
(Mon Jun 05 2017 - 11:28:49 PDT)
Re: [AMBER] AMBER Digest, Vol 1946, Issue 1
(Mon Jun 05 2017 - 08:33:43 PDT)
Garima Singh
Re: [AMBER] AMBER Digest, Vol 1973, Issue 1
(Thu Jun 29 2017 - 04:31:19 PDT)
[AMBER] Amber md in HPC : Job terminated
(Thu Jun 22 2017 - 03:26:49 PDT)
[AMBER] Fwd: SASA calculation
(Mon Jun 12 2017 - 00:07:13 PDT)
[AMBER] SASA calculation
(Thu Jun 08 2017 - 22:40:05 PDT)
Re: [AMBER] AMBER Digest, Vol 1932, Issue 1
(Tue Jun 06 2017 - 01:54:36 PDT)
George Giambasu
Re: [AMBER] Velocity autocorrelation
(Wed Jun 07 2017 - 06:13:22 PDT)
giulia palermo
Re: [AMBER] error running mmpbsa
(Thu Jun 29 2017 - 11:50:00 PDT)
Re: [AMBER] error running mmpbsa
(Tue Jun 27 2017 - 10:53:06 PDT)
Re: [AMBER] error running mmpbsa
(Mon Jun 26 2017 - 16:53:59 PDT)
Re: [AMBER] error running mmpbsa
(Sat Jun 24 2017 - 10:56:40 PDT)
[AMBER] error running mmpbsa
(Fri Jun 23 2017 - 13:32:54 PDT)
Goetz, Andreas
Re: [AMBER] error in qmmm
(Sat Jun 03 2017 - 08:55:43 PDT)
Gorday, Kent M.
[AMBER] Force LEaP to use impose on atoms with LOOP or improper torsions in prep file
(Wed Jun 28 2017 - 11:55:12 PDT)
Gould, Ian R
Re: [AMBER] What nVidia driver for GTX 1080TI?
(Wed Jun 21 2017 - 07:01:14 PDT)
Govind Hegde
Re: [AMBER] LEAP Merging Atom Types
(Wed Jun 21 2017 - 09:12:30 PDT)
Re: [AMBER] LEAP Merging Atom Types
(Wed Jun 21 2017 - 08:52:56 PDT)
[AMBER] LEAP Merging Atom Types
(Tue Jun 20 2017 - 14:10:25 PDT)
Hadházi Ádám
[AMBER] TI/FEP on GPU in Amber?
(Fri Jun 30 2017 - 09:15:48 PDT)
[AMBER] What nVidia driver for GTX 1080TI?
(Wed Jun 21 2017 - 06:22:46 PDT)
Hagrouna sadiki
Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3
(Mon Jun 12 2017 - 07:42:54 PDT)
Hai Nguyen
Re: [AMBER] problem in setting AMBERHOME environment variable using cygwin
(Fri Jun 30 2017 - 10:11:21 PDT)
Re: [AMBER] amber installations error in cygwin
(Fri Jun 30 2017 - 06:37:09 PDT)
Re: [AMBER] using mmgbsa for dna/protein
(Tue Jun 27 2017 - 21:02:35 PDT)
Re: [AMBER] using mmgbsa for dna/protein
(Tue Jun 27 2017 - 21:00:44 PDT)
Re: [AMBER] using mmgbsa for dna/protein
(Tue Jun 27 2017 - 20:26:54 PDT)
Re: [AMBER] Hydrogen bond Average distance
(Thu Jun 22 2017 - 22:22:48 PDT)
Re: [AMBER] "Abort trap 6" error message with tLeap and xLeap
(Wed Jun 21 2017 - 07:37:50 PDT)
Re: [AMBER] convert .nc trajectories to .xyz
(Mon Jun 19 2017 - 12:06:16 PDT)
Re: [AMBER] Is explicit solvent more accurate than implicit solvent?
(Wed Jun 07 2017 - 21:28:39 PDT)
Hannes Loeffler
Re: [AMBER] TI MD simulation
(Fri Jun 02 2017 - 04:14:00 PDT)
Re: [AMBER] TI MD simulation
(Fri Jun 02 2017 - 03:35:51 PDT)
Re: [AMBER] TI free energy calculation errors
(Fri Jun 02 2017 - 00:19:54 PDT)
Re: [AMBER] TI free energy calculation errors
(Thu Jun 01 2017 - 11:56:00 PDT)
hannes.loeffler.stfc.ac.uk
Re: [AMBER] TI in dimeric enzyme
(Thu Jun 08 2017 - 00:30:39 PDT)
Harshavardhan Khare
[AMBER] Accelerated MD: How to reweight secondary structure propensities and radial distribution function?
(Sun Jun 04 2017 - 02:29:55 PDT)
Hector A. Baldoni
Re: [AMBER] Specific GPU for running pmemd.cuda
(Fri Jun 16 2017 - 16:52:49 PDT)
Re: [AMBER] deleting water with ParmEd
(Wed Jun 14 2017 - 13:56:01 PDT)
[AMBER] deleting water with ParmEd
(Wed Jun 14 2017 - 12:44:36 PDT)
Irfan Alibay
Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3
(Mon Jun 12 2017 - 06:31:01 PDT)
Re: [AMBER] Retrieve amd.log/ gamd.log files
(Mon Jun 12 2017 - 05:37:04 PDT)
Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3
(Mon Jun 12 2017 - 05:02:53 PDT)
Re: [AMBER] High pressure fluctuation in isothermal-isobaric ensemble
(Thu Jun 01 2017 - 11:05:18 PDT)
Jag Silwal
[AMBER] ambpdb- Segmentation fault (core dumped)
(Wed Jun 28 2017 - 05:16:12 PDT)
[AMBER] mbondi set up
(Sun Jun 25 2017 - 04:45:15 PDT)
[AMBER] Hydrogen bond Average distance
(Tue Jun 20 2017 - 19:14:12 PDT)
[AMBER] Selecting histidine Protonation state for simulation
(Thu Jun 15 2017 - 08:43:53 PDT)
James Kress
Re: [AMBER] LAMMPS data file to PDB file (off topic)
(Wed Jun 14 2017 - 08:52:24 PDT)
Jason Swails
Re: [AMBER] cphstats Error: Could not open or parse cpin file
(Fri Jun 30 2017 - 20:42:18 PDT)
Re: [AMBER] constant pH MD question
(Thu Jun 29 2017 - 18:53:06 PDT)
Re: [AMBER] adding dummy atom using Parmed API
(Thu Jun 29 2017 - 18:50:58 PDT)
Re: [AMBER] convert psf to top of gmx with parmed
(Sun Jun 25 2017 - 12:18:37 PDT)
Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber.
(Wed Jun 14 2017 - 13:08:12 PDT)
Re: [AMBER] MMPBSA.py with non-standard residues?
(Wed Jun 14 2017 - 13:05:40 PDT)
Re: [AMBER] deleting water with ParmEd
(Wed Jun 14 2017 - 13:03:25 PDT)
Re: [AMBER] MMPBSA.py with non-standard residues?
(Wed Jun 07 2017 - 20:55:52 PDT)
Jerrano Bowleg
Re: [AMBER] Specific GPU for running pmemd.cuda
(Fri Jun 16 2017 - 13:03:48 PDT)
Jewgeni Starikow
[AMBER] A question about handling constraints/restraints with AMBER
(Wed Jun 21 2017 - 06:51:08 PDT)
Jeyaram R A
Re: [AMBER] Error during the installion
(Thu Jun 01 2017 - 06:05:23 PDT)
[AMBER] Error during the installion
(Thu Jun 01 2017 - 05:25:29 PDT)
Jianing Song
Re: [AMBER] External electric fields support for GPU and how to set the parameters in mdin files?
(Tue Jun 06 2017 - 23:59:55 PDT)
[AMBER] External electric fields support for GPU and how to set the parameters in mdin files?
(Tue Jun 06 2017 - 21:49:45 PDT)
Johannes Kalliauer
[AMBER] Leap: Periodic Boundary of DNA
(Wed Jun 21 2017 - 06:44:45 PDT)
Julio Dominguez
Re: [AMBER] Formula/reference for ambertools native contact calculations
(Tue Jun 13 2017 - 19:26:16 PDT)
[AMBER] Formula/reference for ambertools native contact calculations
(Mon Jun 12 2017 - 09:27:54 PDT)
Karl Kirschner
[AMBER] An off topic survey request
(Mon Jun 26 2017 - 04:36:29 PDT)
Re: [AMBER] correlated dihedrals in ff parameterization
(Thu Jun 22 2017 - 03:40:20 PDT)
Kat G
[AMBER] Retrieve amd.log/ gamd.log files
(Fri Jun 09 2017 - 21:00:52 PDT)
Krantzman, Kristin D
Re: [AMBER] Specific GPU for running pmemd.cuda
(Fri Jun 16 2017 - 15:05:14 PDT)
[AMBER] Specific GPU for running pmemd.cuda
(Fri Jun 16 2017 - 12:48:05 PDT)
Loris Moretti
Re: [AMBER] amino-cyclopropyl parameters
(Thu Jun 01 2017 - 06:07:48 PDT)
Re: [AMBER] amino-cyclopropyl parameters
(Thu Jun 01 2017 - 00:37:05 PDT)
Manjula Saravanan
[AMBER] Normal mode entropy calculations for active site residues
(Tue Jun 06 2017 - 19:22:01 PDT)
Marat Talipov
[AMBER] Linear energy decrease in the JAC_production_NVE_4fs benchmark on SDSC Comet (GPU)
(Fri Jun 02 2017 - 07:39:48 PDT)
Marc van der Kamp
Re: [AMBER] MMPBSA.py with non-standard residues?
(Mon Jun 12 2017 - 04:55:07 PDT)
Re: [AMBER] MMPBSA.py with non-standard residues?
(Wed Jun 07 2017 - 23:42:19 PDT)
[AMBER] MMPBSA.py with non-standard residues?
(Mon Jun 05 2017 - 07:35:19 PDT)
Marcos Serrou do Amaral
Re: [AMBER] MD simulation of the whole protein or just its ligand-binding domain
(Tue Jun 06 2017 - 06:45:49 PDT)
Markowska
Re: [AMBER] TI MD simulation
(Fri Jun 02 2017 - 04:25:15 PDT)
Maryam Hamzehee
[AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes
(Wed Jun 21 2017 - 02:23:10 PDT)
Meng Wu
Re: [AMBER] set substrate concentration gradient difference
(Thu Jun 08 2017 - 19:26:45 PDT)
[AMBER] set substrate concentration gradient difference acorss membrane
(Mon Jun 05 2017 - 18:07:47 PDT)
[AMBER] How to set substrate concentration gradient difference acorss membrane
(Fri Jun 02 2017 - 21:37:19 PDT)
Michael Shokhen
Re: [AMBER] constant pH MD question
(Thu Jun 29 2017 - 10:15:20 PDT)
[AMBER] constant pH MD question
(Thu Jun 29 2017 - 02:17:58 PDT)
Miguel Rivera
Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber.
(Wed Jun 07 2017 - 12:22:21 PDT)
Re: [AMBER] pmemd.MPI error on lonestar5 super comp.
(Wed Jun 07 2017 - 12:19:24 PDT)
MOHD HOMAIDUR RAHMAN
Re: [AMBER] Poor performance of REMD simulation
(Wed Jun 07 2017 - 14:43:58 PDT)
[AMBER] Poor performance of REMD simulation
(Wed Jun 07 2017 - 13:54:23 PDT)
Monsurat Lawal
Re: [AMBER] constant pH MD question
(Thu Jun 29 2017 - 02:31:43 PDT)
Mustafa Alhaji Isa
Re: [AMBER] problem in setting AMBERHOME environment variable using cygwin
(Fri Jun 30 2017 - 11:10:47 PDT)
[AMBER] problem in setting AMBERHOME environment variable using cygwin
(Fri Jun 30 2017 - 10:08:10 PDT)
[AMBER] problem of installing amber17 in window 10 using cygwin
(Fri Jun 30 2017 - 08:28:55 PDT)
[AMBER] Download and installing cpptraj sub-application
(Sat Jun 24 2017 - 03:56:00 PDT)
[AMBER] Download and installing cpptraj sub-application
(Sat Jun 24 2017 - 03:56:01 PDT)
[AMBER] problem in creating topology and coordinate files
(Fri Jun 23 2017 - 21:51:35 PDT)
[AMBER] Problem of running ANTECHAMBER
(Fri Jun 23 2017 - 21:19:30 PDT)
[AMBER] Problem in creating topology and coordinate files
(Sat Jun 10 2017 - 22:49:59 PDT)
Re: [AMBER] How restart md simulation
(Sat Jun 10 2017 - 05:24:47 PDT)
[AMBER] How restart md simulation
(Sat Jun 10 2017 - 03:48:55 PDT)
Nikolay N. Kuzmich
Re: [AMBER] MD simulation of the whole protein or just its ligand-binding domain
(Thu Jun 08 2017 - 08:09:23 PDT)
[AMBER] MD simulation of the whole protein or just its ligand-binding domain
(Tue Jun 06 2017 - 02:02:51 PDT)
Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial
(Thu Jun 01 2017 - 09:50:28 PDT)
Núbia Prates
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 11:29:45 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 10:53:40 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 11:06:34 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 10:52:00 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 10:42:01 PDT)
[AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 10:19:01 PDT)
[AMBER] " possible FAILURE " messages
(Wed Jun 21 2017 - 06:41:16 PDT)
Pengfei Li
Re: [AMBER] MCPB step 2 local variable 'ban' referenced before assignment
(Fri Jun 30 2017 - 14:26:47 PDT)
Re: [AMBER] MCPB.py warning meaning is this mol2 file correct??
(Fri Jun 30 2017 - 13:56:03 PDT)
Re: [AMBER] SN is required in naa_mol2files but not provided
(Mon Jun 26 2017 - 08:25:51 PDT)
Pratul K. Agarwal
Re: [AMBER] problem in setting AMBERHOME environment variable using cygwin
(Fri Jun 30 2017 - 17:53:05 PDT)
Re: [AMBER] center of mass of Guanine
(Fri Jun 02 2017 - 06:16:38 PDT)
Qinghua Liao
Re: [AMBER] AMber trajectory to Gromacs trajectory
(Sat Jun 24 2017 - 05:02:03 PDT)
[AMBER] convert psf to top of gmx with parmed
(Wed Jun 21 2017 - 09:42:48 PDT)
Ramin Salimi
[AMBER] Parabolic restraint with nmropt
(Tue Jun 27 2017 - 02:07:50 PDT)
Re: [AMBER] relaxation time to maintain quasi-static condition
(Tue Jun 20 2017 - 12:15:53 PDT)
Re: [AMBER] relaxation time to maintain quasi-static condition
(Tue Jun 20 2017 - 09:40:45 PDT)
[AMBER] relaxation time to maintain quasi-static condition
(Mon Jun 19 2017 - 18:06:12 PDT)
Re: [AMBER] Weired behaviour during Heating
(Fri Jun 16 2017 - 10:52:08 PDT)
[AMBER] Ramin Salimi wants to share the file Heat.tar.gz with you
(Thu Jun 15 2017 - 21:55:14 PDT)
[AMBER] Weired behaviour during Heating
(Thu Jun 15 2017 - 21:55:02 PDT)
Re: [AMBER] Warning during minimization
(Thu Jun 15 2017 - 21:23:25 PDT)
Re: [AMBER] Warning during minimization
(Wed Jun 14 2017 - 22:20:27 PDT)
Re: [AMBER] Warning during minimization
(Wed Jun 14 2017 - 18:28:17 PDT)
[AMBER] Warning during minimization
(Wed Jun 14 2017 - 18:14:57 PDT)
Re: [AMBER] High pressure fluctuation in isothermal-isobaric ensemble
(Thu Jun 01 2017 - 07:36:39 PDT)
Rana Rehan Khalid
Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440
(Thu Jun 29 2017 - 22:03:39 PDT)
Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440
(Thu Jun 29 2017 - 21:38:56 PDT)
Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440
(Thu Jun 29 2017 - 21:26:12 PDT)
Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440
(Thu Jun 29 2017 - 21:15:47 PDT)
Re: [AMBER] kindly see the leap.log for fe---02
(Thu Jun 29 2017 - 21:11:44 PDT)
Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440
(Thu Jun 29 2017 - 20:30:14 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Thu Jun 29 2017 - 20:09:31 PDT)
[AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440
(Thu Jun 29 2017 - 19:44:36 PDT)
[AMBER] how we can find that metal residue protonation state
(Thu Jun 29 2017 - 19:15:48 PDT)
Re: [AMBER] MCPB.py warning meaning is this mol2 file correct??
(Thu Jun 29 2017 - 18:12:44 PDT)
[AMBER] MCPB.py warning meaning is this mol2 file correct??
(Thu Jun 29 2017 - 18:07:09 PDT)
[AMBER] kindly see the leap.log for fe---02
(Thu Jun 29 2017 - 17:16:42 PDT)
Re: [AMBER] antechamber
(Thu Jun 29 2017 - 14:16:58 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Thu Jun 29 2017 - 13:33:28 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Thu Jun 29 2017 - 12:05:31 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 23:27:13 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 23:23:21 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 23:07:18 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 23:06:03 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 22:42:20 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 22:13:59 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 21:56:59 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 21:31:42 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Wed Jun 28 2017 - 21:23:05 PDT)
Re: [AMBER] antechamber
(Wed Jun 28 2017 - 21:08:54 PDT)
[AMBER] Heme parameter error
(Wed Jun 28 2017 - 17:58:03 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Wed Jun 28 2017 - 17:45:46 PDT)
[AMBER] antechamber
(Wed Jun 28 2017 - 15:37:12 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Wed Jun 28 2017 - 15:34:13 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Wed Jun 28 2017 - 13:27:25 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Wed Jun 28 2017 - 12:18:46 PDT)
[AMBER] steps to prepare prmtop and inpcrd for heme containing protein (ff for fe----O2 is present )
(Wed Jun 28 2017 - 12:03:02 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 11:25:20 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 11:24:00 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 11:14:30 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 11:04:55 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 10:54:22 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 10:49:53 PDT)
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 10:30:11 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Wed Jun 28 2017 - 10:28:43 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Wed Jun 28 2017 - 10:17:39 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Tue Jun 27 2017 - 22:59:58 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Tue Jun 27 2017 - 22:43:59 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Tue Jun 27 2017 - 22:33:54 PDT)
Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Tue Jun 27 2017 - 22:11:11 PDT)
[AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein
(Tue Jun 27 2017 - 20:54:07 PDT)
Re: [AMBER] how heme force field combine with amber 99 ff
(Mon Jun 26 2017 - 19:03:23 PDT)
[AMBER] how heme force field combine with amber 99 ff
(Mon Jun 26 2017 - 13:44:56 PDT)
Ray Luo
Re: [AMBER] mmpbsa
(Mon Jun 26 2017 - 15:48:26 PDT)
Robert Molt
Re: [AMBER] Is explicit solvent more accurate than implicit solvent?
(Wed Jun 07 2017 - 17:13:12 PDT)
Robert Wohlhueter
[AMBER] cuda vs. mpi vs. mpi-cuda
(Sun Jun 04 2017 - 12:17:34 PDT)
Ross Walker
Re: [AMBER] TI/FEP on GPU in Amber?
(Fri Jun 30 2017 - 12:59:09 PDT)
Re: [AMBER] Amber14 compatible with TITAN X Pascal?
(Fri Jun 30 2017 - 12:54:58 PDT)
Saikat Pal
[AMBER] Is there any analysis of the stability of DNA in presence of Divalent cation??
(Thu Jun 29 2017 - 06:58:11 PDT)
Re: [AMBER] AMber trajectory to Gromacs trajectory
(Mon Jun 26 2017 - 06:30:27 PDT)
Re: [AMBER] AMber trajectory to Gromacs trajectory
(Sun Jun 25 2017 - 22:06:07 PDT)
[AMBER] AMber trajectory to Gromacs trajectory
(Sat Jun 24 2017 - 04:55:25 PDT)
Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB
(Fri Jun 16 2017 - 00:04:48 PDT)
Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB
(Thu Jun 15 2017 - 07:39:33 PDT)
Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB
(Thu Jun 15 2017 - 03:38:27 PDT)
[AMBER] problem regarding ACE capping of the protein terminal of the PDB
(Thu Jun 15 2017 - 00:29:46 PDT)
Re: [AMBER] Center of mass
(Wed Jun 07 2017 - 09:29:22 PDT)
[AMBER] Center of mass
(Wed Jun 07 2017 - 03:51:55 PDT)
Re: [AMBER] Center of mass
(Tue Jun 06 2017 - 21:34:28 PDT)
[AMBER] Center of mass
(Tue Jun 06 2017 - 07:56:22 PDT)
[AMBER] center of mass of Guanine
(Fri Jun 02 2017 - 05:25:42 PDT)
Saman Yousuf ali
[AMBER] average no. of H bond between ligand-solvent.
(Tue Jun 06 2017 - 05:02:31 PDT)
Scott Brozell
Re: [AMBER] TI free energy calculation errors
(Thu Jun 29 2017 - 20:03:35 PDT)
Re: [AMBER] MCPB step 2 local variable 'ban' referenced before assignment
(Thu Jun 29 2017 - 12:24:02 PDT)
Shafaq Muzammal
Re: [AMBER] convert .nc trajectories to .xyz
(Fri Jun 16 2017 - 08:19:59 PDT)
[AMBER] convert .nc trajectories to .xyz
(Wed Jun 14 2017 - 01:29:15 PDT)
Re: [AMBER] Split trajectory
(Sun Jun 11 2017 - 09:29:55 PDT)
[AMBER] Split trajectory
(Sun Jun 11 2017 - 05:32:43 PDT)
Re: [AMBER] How restart md simulation
(Sat Jun 10 2017 - 04:07:43 PDT)
SHAILESH KUMAR
Re: [AMBER] sander do not write rst and mdcrd files
(Wed Jun 28 2017 - 11:12:16 PDT)
Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time
(Wed Jun 28 2017 - 11:02:22 PDT)
Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time
(Fri Jun 23 2017 - 03:55:27 PDT)
Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time
(Thu Jun 22 2017 - 09:47:41 PDT)
[AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time
(Thu Jun 22 2017 - 06:51:00 PDT)
Sonia Ziada
Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3
(Mon Jun 12 2017 - 08:08:00 PDT)
Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3
(Mon Jun 12 2017 - 07:36:55 PDT)
Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3
(Mon Jun 12 2017 - 05:53:01 PDT)
[AMBER] Fwd: Accelerated MD when iamd=1 or 3
(Mon Jun 12 2017 - 04:45:41 PDT)
[AMBER] Accelerated MD when iamd=1 or 3
(Sun Jun 11 2017 - 02:38:56 PDT)
[AMBER] accelerated molecular dynamics when iamd=1 or iamd=3
(Sun Jun 04 2017 - 08:39:21 PDT)
Sowmya Indrakumar
Re: [AMBER] TI MD simulation
(Fri Jun 02 2017 - 05:28:15 PDT)
Re: [AMBER] TI MD simulation
(Fri Jun 02 2017 - 03:57:33 PDT)
[AMBER] TI MD simulation
(Fri Jun 02 2017 - 03:24:48 PDT)
Sumudu Leelananda
Re: [AMBER] TI free energy calculation errors
(Wed Jun 28 2017 - 12:53:32 PDT)
Re: [AMBER] TI free energy calculation errors
(Wed Jun 28 2017 - 12:47:04 PDT)
Re: [AMBER] TI free energy calculation errors
(Wed Jun 28 2017 - 12:29:38 PDT)
Re: [AMBER] TI free energy calculation errors
(Wed Jun 28 2017 - 12:05:13 PDT)
Re: [AMBER] TI free energy calculation errors
(Wed Jun 28 2017 - 09:18:26 PDT)
Re: [AMBER] TI free energy calculation errors
(Thu Jun 01 2017 - 12:22:53 PDT)
[AMBER] TI free energy calculation errors
(Thu Jun 01 2017 - 11:16:38 PDT)
Supriyo Naskar
Re: [AMBER] RNA parameters for wc_helix
(Tue Jun 13 2017 - 00:13:25 PDT)
Re: [AMBER] RNA parameters for wc_helix
(Mon Jun 12 2017 - 07:10:02 PDT)
[AMBER] RNA parameters for wc_helix
(Mon Jun 12 2017 - 02:11:53 PDT)
[AMBER] Calculation of Volume fraction
(Tue Jun 06 2017 - 06:12:51 PDT)
Sushi Shilpa
[AMBER] LAMMPS data file to PDB file (off topic)
(Tue Jun 13 2017 - 21:29:22 PDT)
Thakur, Abhishek
[AMBER] Amber14 compatible with TITAN X Pascal?
(Fri Jun 30 2017 - 09:43:38 PDT)
[AMBER] visualizing first mode of motion from PCA analysis in chimera or vmd
(Thu Jun 08 2017 - 14:16:38 PDT)
Re: [AMBER] PCA analysis
(Thu Jun 08 2017 - 11:33:58 PDT)
[AMBER] PCA analysis
(Thu Jun 08 2017 - 09:52:06 PDT)
[AMBER] RMSD
(Mon Jun 05 2017 - 14:19:23 PDT)
Thomas Cheatham
Re: [AMBER] Poor performance of REMD simulation
(Wed Jun 07 2017 - 20:00:55 PDT)
Thomas Evangelidis
[AMBER] adding dummy atom using Parmed API
(Thu Jun 29 2017 - 16:08:52 PDT)
venkat
Re: [AMBER] amber installations error in cygwin
(Fri Jun 30 2017 - 22:53:25 PDT)
[AMBER] amber installations error in cygwin
(Fri Jun 30 2017 - 06:30:01 PDT)
Vidhya Srivatsan
Re: [AMBER] cuda vs. mpi vs. mpi-cuda
(Mon Jun 05 2017 - 06:23:53 PDT)
Re: [AMBER] cuda vs. mpi vs. mpi-cuda
(Mon Jun 05 2017 - 04:39:15 PDT)
Vincent Ustach
[AMBER] cphstats Error: Could not open or parse cpin file
(Fri Jun 30 2017 - 15:54:52 PDT)
Vishal Nemaysh
Re: [AMBER] Regarding empty lig.frcmod file
(Fri Jun 16 2017 - 05:44:10 PDT)
Re: [AMBER] Regarding empty lig.frcmod file
(Fri Jun 16 2017 - 00:30:55 PDT)
Re: [AMBER] Regarding empty lig.frcmod file
(Thu Jun 15 2017 - 10:35:51 PDT)
Re: [AMBER] Regarding empty lig.frcmod file
(Fri Jun 09 2017 - 05:45:54 PDT)
Re: [AMBER] Regarding empty lig.frcmod file
(Fri Jun 09 2017 - 04:44:51 PDT)
Re: [AMBER] Regarding empty lig.frcmod file
(Fri Jun 09 2017 - 00:20:58 PDT)
[AMBER] Regarding empty lig.frcmod file
(Tue Jun 06 2017 - 09:27:45 PDT)
waleed zalloum
[AMBER] Free energy path
(Mon Jun 19 2017 - 18:22:28 PDT)
Xichong Liu
Re: [AMBER] "Abort trap 6" error message with tLeap and xLeap
(Wed Jun 21 2017 - 13:53:23 PDT)
Re: [AMBER] "Abort trap 6" error message with tLeap and xLeap
(Wed Jun 21 2017 - 06:53:20 PDT)
[AMBER] "Abort trap 6" error message with tLeap and xLeap
(Wed Jun 21 2017 - 04:36:11 PDT)
Yue Qian
Re: [AMBER] Neutral N-terminal proline parameter in AMBER force field
(Tue Jun 13 2017 - 07:05:47 PDT)
[AMBER] Neutral N-terminal proline in AMBER force field
(Wed Jun 07 2017 - 07:48:51 PDT)
刘兰茹
[AMBER] can't mutated Pro to Ala correctly during generating snapshots
(Mon Jun 26 2017 - 20:32:30 PDT)
Last message date
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Fri Jun 30 2017 - 23:00:03 PDT
Archived on
: Fri Dec 20 2024 - 05:55:34 PST
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