Amber Archive Apr 2016: by author

ABEL Stephane 175950
- Re: [AMBER] MD simulations of deprotonated tyrosine residue with AMBER (Mon Apr 04 2016 - 06:55:55 PDT)
- [AMBER] MD simulations of deprotonated tyrosine residue with AMBER (Mon Apr 04 2016 - 06:22:41 PDT)
- Re: [AMBER] Introducing the exciting next step in MD software development (Fri Apr 01 2016 - 03:55:00 PDT)
ABHIJEET CHOWDHURY
- Re: [AMBER] query regarding -refc (Sun Apr 10 2016 - 23:02:59 PDT)
- [AMBER] query regarding -refc (Sun Apr 10 2016 - 21:11:07 PDT)
- Re: [AMBER] Amber: .rst file not created (Thu Apr 07 2016 - 04:47:27 PDT)
- [AMBER] Amber: .rst file not created (Wed Apr 06 2016 - 05:08:56 PDT)
Adrian Roitberg
- Re: [AMBER] The question about SMD (Tue Apr 05 2016 - 07:23:47 PDT)
- Re: [AMBER] MD simulations of deprotonated tyrosine residue with AMBER (Mon Apr 04 2016 - 06:31:22 PDT)
- Re: [AMBER] Introducing the exciting next step in MD software development (Fri Apr 01 2016 - 06:36:36 PDT)
- Re: [AMBER] Introducing the exciting next step in MD software development (Fri Apr 01 2016 - 04:31:02 PDT)
Aishani Prem
- Re: [AMBER] Modelling of proteins (Fri Apr 22 2016 - 11:56:18 PDT)
- [AMBER] Modelling of proteins (Thu Apr 14 2016 - 14:30:00 PDT)
Alessandro Contini
- Re: [AMBER] MMPBSA : Calculation when keeping explicit water molecules (Fri Apr 08 2016 - 05:38:24 PDT)
Amika Sood
- [AMBER] Quasi-harmonic calculation (Wed Apr 13 2016 - 06:15:06 PDT)
Amy Rice
- Re: [AMBER] Cpptraj LipidOrder error: mask groups are not the same length (Thu Apr 28 2016 - 12:29:44 PDT)
- [AMBER] Cpptraj LipidOrder error: mask groups are not the same length (Thu Apr 28 2016 - 11:30:14 PDT)
Andrew Schaub
- Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber (Sat Apr 30 2016 - 22:01:04 PDT)
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion (Sat Apr 23 2016 - 11:41:21 PDT)
Andy Watkins
- Re: [AMBER] RMSD graph for protein-RNA complex (Tue Apr 12 2016 - 22:12:30 PDT)
Anna Cebrian Prats
- Re: [AMBER] tleap - protein + ligand + heme group (Fri Apr 29 2016 - 08:16:21 PDT)
- [AMBER] tleap - protein + ligand + heme group (Thu Apr 28 2016 - 08:52:13 PDT)
- [AMBER] HEME group in a protein (Tue Apr 19 2016 - 04:14:45 PDT)
anu chandra
- [AMBER] Force field parameters for glycerophophate (Wed Apr 20 2016 - 15:24:47 PDT)
- Re: [AMBER] Approach for transmembrane protein (Tue Apr 19 2016 - 08:07:39 PDT)
Arati Paudyal
- Re: [AMBER] ambpdb error (Fri Apr 29 2016 - 10:01:20 PDT)
- Re: [AMBER] ambpdb error (Fri Apr 29 2016 - 08:25:42 PDT)
- [AMBER] ambpdb error (Fri Apr 29 2016 - 06:41:40 PDT)
- Re: [AMBER] Change PBRadii after simulation (Mon Apr 18 2016 - 06:34:50 PDT)
- Re: [AMBER] Amber script to delete all hydrogen atoms from protein? (Sun Apr 10 2016 - 04:22:31 PDT)
- Re: [AMBER] Error -per residue Energy Decomposition (Sat Apr 09 2016 - 16:56:24 PDT)
- [AMBER] Error -per residue Energy Decomposition (Fri Apr 08 2016 - 12:12:41 PDT)
Arjun Sharma
- [AMBER] amber v16 (Mon Apr 18 2016 - 12:38:01 PDT)
ATUL KUMAR
- [AMBER] problem in 3DRISM convergence (Wed Apr 20 2016 - 03:29:41 PDT)
- [AMBER] Error in 3DRISM calculation (Sun Apr 17 2016 - 22:46:49 PDT)
Avik Bhattacharjee
- Re: [AMBER] facing problems simulating in implicit solvent (Sat Apr 16 2016 - 10:20:02 PDT)
- [AMBER] facing problems simulating in implicit solvent (Sat Apr 16 2016 - 09:43:42 PDT)
Ayesha Fatima
- Re: [AMBER] qmmm mmpbsa spin multiplicity problem (Thu Apr 21 2016 - 19:18:16 PDT)
- [AMBER] qmmm mmpbsa spin multiplicity problem (Thu Apr 21 2016 - 08:32:28 PDT)
Ayesha Kanwal
- [AMBER] error while putting the whole path into python script (Wed Apr 20 2016 - 00:37:51 PDT)
- Re: [AMBER] query about .mdcrd file (Tue Apr 19 2016 - 23:12:36 PDT)
- Re: [AMBER] query about .mdcrd file (Tue Apr 19 2016 - 10:12:36 PDT)
- [AMBER] query about .mdcrd file (Tue Apr 19 2016 - 04:23:44 PDT)
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file (Tue Apr 19 2016 - 03:38:58 PDT)
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file (Tue Apr 19 2016 - 03:32:31 PDT)
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file (Tue Apr 19 2016 - 03:16:13 PDT)
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file (Tue Apr 19 2016 - 03:01:53 PDT)
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file (Tue Apr 19 2016 - 02:59:01 PDT)
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file (Tue Apr 19 2016 - 02:21:44 PDT)
- [AMBER] want to ask you about MMPBSA.py .mdcrd file (Tue Apr 19 2016 - 00:55:36 PDT)
- Re: [AMBER] how to embed amber14 (Mon Apr 18 2016 - 03:47:23 PDT)
- [AMBER] how to embed amber14 (Thu Apr 14 2016 - 03:34:57 PDT)
Balaji Selvam
- [AMBER] Implicit Solvent simulation - membrane proteins (Mon Apr 11 2016 - 10:51:35 PDT)
Batuhan Kav
- Re: [AMBER] Error while converting CHARMM-GUI generated file (Mon Apr 25 2016 - 06:39:47 PDT)
- Re: [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file (Fri Apr 15 2016 - 05:28:29 PDT)
- [AMBER] geometric center with cpptraj (Mon Apr 11 2016 - 03:00:52 PDT)
- [AMBER] turning of non-bonded interactions with addExclusions (Mon Apr 04 2016 - 02:42:30 PDT)
Beale, John
- Re: [AMBER] Antechamber Problem (Wed Apr 13 2016 - 00:47:28 PDT)
- [AMBER] Antechamber Problem (Wed Apr 13 2016 - 00:18:07 PDT)
Bill Miller III
- Re: [AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm (Fri Apr 01 2016 - 05:22:32 PDT)
Bill Ross
- Re: [AMBER] CUDA and restraint (Fri Apr 29 2016 - 01:28:22 PDT)
- Re: [AMBER] CUDA and restraint (Fri Apr 29 2016 - 01:25:32 PDT)
- Re: [AMBER] fortran i/o on system shared memory (Thu Apr 28 2016 - 23:31:13 PDT)
- [AMBER] fortran i/o on system shared memory (Thu Apr 28 2016 - 23:20:53 PDT)
- Re: [AMBER] No torsion terms for CB-N*-CR-H5 (Thu Apr 28 2016 - 01:14:05 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Sun Apr 24 2016 - 15:46:55 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Sat Apr 23 2016 - 11:55:45 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Sat Apr 23 2016 - 11:53:25 PDT)
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion (Sat Apr 23 2016 - 11:50:33 PDT)
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion (Sat Apr 23 2016 - 11:30:51 PDT)
- Re: [AMBER] Modelling of proteins (Fri Apr 22 2016 - 12:03:07 PDT)
- Re: [AMBER] XLeap didn't save the parameter file (Fri Apr 22 2016 - 09:28:56 PDT)
- Re: [AMBER] interactive MD applied to AI (Thu Apr 21 2016 - 20:16:19 PDT)
- Re: [AMBER] How to deal with monoatomic ion, such as ILs cation (Thu Apr 21 2016 - 18:39:21 PDT)
- Re: [AMBER] interactive MD applied to AI (Thu Apr 21 2016 - 18:37:27 PDT)
- Re: [AMBER] interactive MD applied to AI (Thu Apr 21 2016 - 17:25:58 PDT)
- Re: [AMBER] Building Cyclic Peptide in xleap (Thu Apr 21 2016 - 16:53:42 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Thu Apr 21 2016 - 11:22:16 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Thu Apr 21 2016 - 11:10:07 PDT)
- Re: [AMBER] XLeap didn't save the parameter file (Wed Apr 20 2016 - 01:33:09 PDT)
- Re: [AMBER] error while putting the whole path into python script (Wed Apr 20 2016 - 01:00:09 PDT)
- [AMBER] interactive MD applied to AI (Tue Apr 19 2016 - 12:19:05 PDT)
- Re: [AMBER] LEAP RUN FAILED (Thu Apr 14 2016 - 04:10:10 PDT)
- Re: [AMBER] mm_pbsa.pl ERROR (Thu Apr 14 2016 - 01:44:49 PDT)
- Re: [AMBER] Regarding Input file preparation in AMBER (Thu Apr 14 2016 - 00:40:20 PDT)
- Re: [AMBER] Antechamber Problem (Wed Apr 13 2016 - 01:15:47 PDT)
- Re: [AMBER] Antechamber Problem (Wed Apr 13 2016 - 00:42:09 PDT)
- Re: [AMBER] Multiple restraints for minimization (Mon Apr 11 2016 - 11:53:15 PDT)
- Re: [AMBER] sander number of atoms limit (Tue Apr 05 2016 - 02:26:13 PDT)
- Re: [AMBER] build a phosphorylated protein structure pdb file (Mon Apr 04 2016 - 18:34:03 PDT)
- Re: [AMBER] Introducing the exciting next step in MD software development (Fri Apr 01 2016 - 06:34:19 PDT)
Brent Krueger
- Re: [AMBER] Run Stage 2 of the RESP fit (Sun Apr 03 2016 - 06:49:40 PDT)
- Re: [AMBER] Introducing the exciting next step in MD software development (Fri Apr 01 2016 - 04:05:04 PDT)
Brett
- [AMBER] protein complex dissociation during md (Mon Apr 25 2016 - 06:54:34 PDT)
- [AMBER] warning message for antechamber by acpype (Wed Apr 20 2016 - 07:41:28 PDT)
- [AMBER] on antechamber (Mon Apr 18 2016 - 02:28:10 PDT)
- [AMBER] on antechamber (Sun Apr 17 2016 - 23:38:26 PDT)
- [AMBER] on the MD of protein-ligand (Thu Apr 07 2016 - 22:48:53 PDT)
Brett
- [AMBER] on antechamber (Sat Apr 30 2016 - 02:00:14 PDT)
Brian Radak
- Re: [AMBER] Energies in QM/MM MD (Mon Apr 25 2016 - 16:50:45 PDT)
Carlos Simmerling
- Re: [AMBER] Targeted MD error (Thu Apr 28 2016 - 10:03:03 PDT)
- Re: [AMBER] Hydroxyproline (Sat Apr 23 2016 - 05:36:26 PDT)
- Re: [AMBER] Change PBRadii after simulation (Mon Apr 18 2016 - 06:04:05 PDT)
- Re: [AMBER] Change PBRadii after simulation (Sun Apr 17 2016 - 04:53:37 PDT)
- Re: [AMBER] Change PBRadii after simulation (Sat Apr 16 2016 - 20:33:43 PDT)
- Re: [AMBER] facing problems simulating in implicit solvent (Sat Apr 16 2016 - 10:42:37 PDT)
- Re: [AMBER] Protein-DNA docking (Tue Apr 12 2016 - 13:50:46 PDT)
- Re: [AMBER] ff12SB force field (Mon Apr 11 2016 - 06:50:55 PDT)
- Re: [AMBER] Metal geometry (Fri Apr 08 2016 - 07:32:51 PDT)
- Re: [AMBER] build a phosphorylated protein structure pdb file (Mon Apr 04 2016 - 03:10:17 PDT)
- Re: [AMBER] Problems with periodic boundaries (Fri Apr 01 2016 - 13:38:42 PDT)
- Re: [AMBER] Problems with periodic boundaries (Fri Apr 01 2016 - 12:40:51 PDT)
- Re: [AMBER] Relation between binding affinity and free enegy (Fri Apr 01 2016 - 07:15:45 PDT)
CHAMI F.
- [AMBER] Fortran Modernisation Workshop - Numerical Algorithms Group NAG (Fri Apr 15 2016 - 03:23:45 PDT)
Charles Lin
- Re: [AMBER] CUDA and restraint (Fri Apr 29 2016 - 04:52:35 PDT)
- Re: [AMBER] Targeted MD error (Thu Apr 28 2016 - 09:56:57 PDT)
- Re: [AMBER] CUDA and restraint (Thu Apr 28 2016 - 09:27:00 PDT)
- Re: [AMBER] General question (Tue Apr 05 2016 - 22:57:17 PDT)
- Re: [AMBER] General question (Tue Apr 05 2016 - 21:43:16 PDT)
Chitrak Gupta
- [AMBER] CHAMBER error for the updated CHARMM36 force fields (Tue Apr 12 2016 - 08:23:46 PDT)
Chris Moth
- Re: [AMBER] Cpptraj LipidOrder error: mask groups are not the same length (Thu Apr 28 2016 - 11:53:45 PDT)
- Re: [AMBER] Introducing the exciting next step in MD software development (Fri Apr 01 2016 - 06:20:34 PDT)
Christina Bergonzo
- Re: [AMBER] building DNA with extruded base (Tue Apr 19 2016 - 11:56:54 PDT)
- Re: [AMBER] query about .mdcrd file (Tue Apr 19 2016 - 10:27:08 PDT)
Cortopassi, Wilian
- Re: [AMBER] Electrostatic Energies - MMPBSA (Wed Apr 20 2016 - 04:04:24 PDT)
- [AMBER] Electrostatic Energies - MMPBSA (Tue Apr 19 2016 - 13:55:24 PDT)
- [AMBER] MMGBSA and dielectric constants (Wed Apr 13 2016 - 09:37:34 PDT)
CRISTIAN ROSSI PERARO
- Re: [AMBER] mm_pbsa.pl, that I'm doing this right? (Mon Apr 11 2016 - 12:07:42 PDT)
- [AMBER] mm_pbsa.pl, that I'm doing this right? (Sun Apr 10 2016 - 11:17:32 PDT)
- Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 (Sat Apr 09 2016 - 10:49:56 PDT)
- Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 (Fri Apr 08 2016 - 20:32:49 PDT)
- [AMBER] How to prepare files cyclodextrin to use witch glycam04 (Fri Apr 08 2016 - 19:35:28 PDT)
Damiano Spadoni
- Re: [AMBER] Both positional and distance restraints (Mon Apr 18 2016 - 11:46:39 PDT)
- [AMBER] Both positional and distance restraints (Wed Apr 13 2016 - 06:59:06 PDT)
Daniel Roe
- Re: [AMBER] accelerated MD on set of dihedrals (Fri Apr 29 2016 - 10:18:41 PDT)
- Re: [AMBER] ambpdb error (Fri Apr 29 2016 - 10:14:31 PDT)
- Re: [AMBER] ambpdb error (Fri Apr 29 2016 - 09:17:28 PDT)
- Re: [AMBER] ambpdb error (Fri Apr 29 2016 - 09:16:03 PDT)
- Re: [AMBER] ambpdb error (Fri Apr 29 2016 - 08:27:56 PDT)
- Re: [AMBER] Calculate Percentage of Hydrogen Occurrence (Fri Apr 29 2016 - 08:24:33 PDT)
- Re: [AMBER] ambpdb error (Fri Apr 29 2016 - 07:21:44 PDT)
- Re: [AMBER] Problem in calculating auto time correlation function with ptraj (Wed Apr 27 2016 - 09:26:16 PDT)
- Re: [AMBER] AMBER Project (Tue Apr 26 2016 - 11:54:23 PDT)
- Re: [AMBER] parmed.py (Tue Apr 26 2016 - 08:14:35 PDT)
- Re: [AMBER] Read/visualize volmap output (opendx) (Mon Apr 25 2016 - 12:41:02 PDT)
- Re: [AMBER] rotation angle around an axes (Mon Apr 25 2016 - 10:59:24 PDT)
- Re: [AMBER] Read/visualize volmap output (opendx) (Mon Apr 25 2016 - 07:41:47 PDT)
- Re: [AMBER] Regarding atom types (Thu Apr 21 2016 - 10:16:48 PDT)
- Re: [AMBER] cpptraj SolventAcc and ligand distance plotting (Wed Apr 20 2016 - 13:21:57 PDT)
- Re: [AMBER] cpptraj SolventAcc and ligand distance plotting (Tue Apr 19 2016 - 09:02:48 PDT)
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj (Tue Apr 19 2016 - 09:00:24 PDT)
- Re: [AMBER] [cpptraj] Automating pcmin/pcmax selection of modes command (Tue Apr 19 2016 - 08:49:31 PDT)
- Re: [AMBER] cpptraj SolventAcc and ligand distance plotting (Mon Apr 18 2016 - 07:33:23 PDT)
- Re: [AMBER] on antechamber (Mon Apr 18 2016 - 07:24:29 PDT)
- Re: [AMBER] facing problems simulating in implicit solvent (Sat Apr 16 2016 - 09:50:43 PDT)
- Re: [AMBER] hbond analysis of phosphotyrosine (Sat Apr 16 2016 - 09:38:45 PDT)
- Re: [AMBER] How can I extract PDB files from a molecular dynamics simulation (Fri Apr 15 2016 - 08:42:17 PDT)
- Re: [AMBER] hbond analysis of phosphotyrosine (Fri Apr 15 2016 - 08:35:34 PDT)
- Re: [AMBER] RMSD graph for protein-RNA complex (Wed Apr 13 2016 - 05:01:25 PDT)
- Re: [AMBER] RMSD graph for protein-RNA complex (Tue Apr 12 2016 - 12:50:46 PDT)
- Re: [AMBER] Box dimensions (Mon Apr 11 2016 - 19:44:09 PDT)
- Re: [AMBER] Multiple restraints for minimization (Mon Apr 11 2016 - 12:34:55 PDT)
- Re: [AMBER] Multiple restraints for minimization (Mon Apr 11 2016 - 10:08:54 PDT)
- Re: [AMBER] Box dimensions (Mon Apr 11 2016 - 09:40:29 PDT)
- Re: [AMBER] Could not find angle parameter (Mon Apr 11 2016 - 09:35:43 PDT)
- Re: [AMBER] query regarding dssp plot cpptraj. (Sun Apr 10 2016 - 08:04:29 PDT)
- Re: [AMBER] PCA (Fri Apr 08 2016 - 09:34:11 PDT)
- Re: [AMBER] RMSD graph for protein-RNA complex (Fri Apr 08 2016 - 09:14:32 PDT)
- Re: [AMBER] Hbond command use with non-hydrogen bonds (Thu Apr 07 2016 - 08:39:34 PDT)
- Re: [AMBER] cpptraj: reading in previously created covariance matrix (Tue Apr 05 2016 - 13:12:42 PDT)
- Re: [AMBER] Problems with periodic boundaries (Fri Apr 01 2016 - 10:51:38 PDT)
David A Case
- [AMBER] Release of Amber16 and AmberTools16 (Sat Apr 30 2016 - 09:27:51 PDT)
- Re: [AMBER] on antechamber (Sat Apr 30 2016 - 05:16:06 PDT)
- Re: [AMBER] tleap - protein + ligand + heme group (Fri Apr 29 2016 - 09:27:28 PDT)
- Re: [AMBER] tleap - protein + ligand + heme group (Thu Apr 28 2016 - 10:28:36 PDT)
- Re: [AMBER] Problem in calculating auto time correlation function with ptraj (Wed Apr 27 2016 - 18:20:55 PDT)
- Re: [AMBER] Question about RESP with iodine (Wed Apr 27 2016 - 05:26:19 PDT)
- Re: [AMBER] debug issue (Wed Apr 27 2016 - 05:20:07 PDT)
- Re: [AMBER] No torsion terms for CB-N*-CR-H5 (Sun Apr 24 2016 - 17:33:16 PDT)
- Re: [AMBER] Hydroxyproline (Sat Apr 23 2016 - 05:38:51 PDT)
- Re: [AMBER] XLeap didn't save the parameter file (Fri Apr 22 2016 - 10:38:45 PDT)
- Re: [AMBER] Building Cyclic Peptide in xleap (Thu Apr 21 2016 - 16:35:06 PDT)
- Re: [AMBER] warning message for antechamber by acpype (Thu Apr 21 2016 - 12:26:40 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Thu Apr 21 2016 - 05:14:54 PDT)
- Re: [AMBER] questions about energy terms of amber MD (Thu Apr 21 2016 - 05:05:40 PDT)
- Re: [AMBER] problem in 3DRISM convergence (Wed Apr 20 2016 - 05:17:23 PDT)
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj (Wed Apr 20 2016 - 05:09:30 PDT)
- Re: [AMBER] XLeap didn't save the parameter file (Wed Apr 20 2016 - 05:04:54 PDT)
- Re: [AMBER] building DNA with extruded base (Tue Apr 19 2016 - 11:24:03 PDT)
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj (Tue Apr 19 2016 - 11:20:14 PDT)
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj (Tue Apr 19 2016 - 06:20:00 PDT)
- Re: [AMBER] HEME group in a protein (Tue Apr 19 2016 - 04:41:03 PDT)
- Re: [AMBER] Quasi-harmonic calculation (Mon Apr 18 2016 - 04:35:41 PDT)
- Re: [AMBER] Both positional and distance restraints (Mon Apr 18 2016 - 04:31:18 PDT)
- Re: [AMBER] how to embed amber14 (Mon Apr 18 2016 - 04:26:23 PDT)
- Re: [AMBER] on antechamber (Mon Apr 18 2016 - 04:24:15 PDT)
- Re: [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file (Fri Apr 15 2016 - 05:03:10 PDT)
- Re: [AMBER] hbond analysis of phosphotyrosine (Fri Apr 15 2016 - 04:59:26 PDT)
- Re: [AMBER] mm_pbsa.pl ERROR (Thu Apr 14 2016 - 04:45:32 PDT)
- Re: [AMBER] Natural bond orbital analysis (Wed Apr 13 2016 - 17:59:49 PDT)
- Re: [AMBER] Could not find angle parameter (Wed Apr 13 2016 - 05:34:49 PDT)
- Re: [AMBER] RMSD graph for protein-RNA complex (Wed Apr 13 2016 - 05:23:55 PDT)
- Re: [AMBER] RMSD graph for protein-RNA complex (Tue Apr 12 2016 - 04:45:25 PDT)
- Re: [AMBER] Refinement in explicit solvent (Mon Apr 11 2016 - 05:23:05 PDT)
- Re: [AMBER] RMSD graph for protein-RNA complex (Fri Apr 08 2016 - 04:31:53 PDT)
- Re: [AMBER] General Type Improper Dihedrals vs. Specifics (Wed Apr 06 2016 - 17:46:43 PDT)
- Re: [AMBER] sander number of atoms limit (Tue Apr 05 2016 - 09:13:11 PDT)
- Re: [AMBER] build a phosphorylated protein structure pdb file (Mon Apr 04 2016 - 18:50:05 PDT)
- Re: [AMBER] General question (Mon Apr 04 2016 - 06:01:39 PDT)
- Re: [AMBER] QM calculation (Mon Apr 04 2016 - 05:54:03 PDT)
- Re: [AMBER] QM calculation (Sun Apr 03 2016 - 06:05:25 PDT)
- Re: [AMBER] Hydrophobic solution environment ??? (Sat Apr 02 2016 - 07:59:20 PDT)
- Re: [AMBER] QM calculation (Sat Apr 02 2016 - 07:56:39 PDT)
- Re: [AMBER] Problems with periodic boundaries (Sat Apr 02 2016 - 07:53:51 PDT)
- Re: [AMBER] hoogsteen base pair (Fri Apr 01 2016 - 09:32:47 PDT)
- [AMBER] A contrarian note about gravity potentials in MD (Fri Apr 01 2016 - 09:21:01 PDT)
- Re: [AMBER] Problems running MD simulation using residual dipolar couplings as restraints (Fri Apr 01 2016 - 06:20:15 PDT)
David Cerutti
- Re: [AMBER] Building Cyclic Peptide in xleap (Fri Apr 22 2016 - 09:52:09 PDT)
- Re: [AMBER] Modelling of proteins (Thu Apr 14 2016 - 14:42:52 PDT)
- Re: [AMBER] ff12SB force field (Mon Apr 11 2016 - 13:48:59 PDT)
- Re: [AMBER] query regarding -refc (Mon Apr 11 2016 - 05:58:12 PDT)
- Re: [AMBER] query regarding -refc (Sun Apr 10 2016 - 21:29:53 PDT)
- Re: [AMBER] Is it possible to run TI with pmemd using the AMOEBA force field? (Sun Apr 10 2016 - 19:36:29 PDT)
- Re: [AMBER] Metal geometry (Fri Apr 08 2016 - 08:01:26 PDT)
- Re: [AMBER] on the MD of protein-ligand (Thu Apr 07 2016 - 23:08:13 PDT)
- Re: [AMBER] General Type Improper Dihedrals vs. Specifics (Wed Apr 06 2016 - 18:25:15 PDT)
- Re: [AMBER] General Type Improper Dihedrals vs. Specifics (Wed Apr 06 2016 - 14:50:37 PDT)
- [AMBER] Any issues if I make PMEMD understand bonds span imaging? (Wed Apr 06 2016 - 13:49:28 PDT)
- Re: [AMBER] spherical restraint flatwell potentials (Mon Apr 04 2016 - 12:33:29 PDT)
- Re: [AMBER] spherical restraint flatwell potentials (Mon Apr 04 2016 - 11:32:18 PDT)
- Re: [AMBER] General question (Sun Apr 03 2016 - 23:19:53 PDT)
Dickson, Callum J
- Re: [AMBER] aMD ruins membrane structure (Mon Apr 04 2016 - 07:11:11 PDT)
Domenico Marson
- Re: [AMBER] CUDA and restraint (Fri Apr 29 2016 - 06:37:19 PDT)
- Re: [AMBER] CUDA and restraint (Fri Apr 29 2016 - 02:35:06 PDT)
- Re: [AMBER] CUDA and restraint (Fri Apr 29 2016 - 01:19:41 PDT)
- [AMBER] CUDA and restraint (Thu Apr 28 2016 - 03:31:34 PDT)
- [AMBER] CUDA and restraint (Fri Apr 22 2016 - 02:21:43 PDT)
Dr. Andreas W. Goetz
- Re: [AMBER] Energies in QM/MM MD (Tue Apr 26 2016 - 16:02:20 PDT)
Dr. Anselm Horn
- Re: [AMBER] protein complex dissociation during md (Fri Apr 29 2016 - 01:56:27 PDT)
- Re: [AMBER] RMSD graph for protein-RNA complex (Fri Apr 08 2016 - 02:30:14 PDT)
Dr. M. Shahid
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Mon Apr 25 2016 - 05:31:51 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Thu Apr 21 2016 - 02:29:41 PDT)
- Re: [AMBER] query about .mdcrd file (Tue Apr 19 2016 - 05:48:20 PDT)
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file (Tue Apr 19 2016 - 03:04:39 PDT)
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file (Tue Apr 19 2016 - 02:47:02 PDT)
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file (Tue Apr 19 2016 - 01:12:40 PDT)
Dwight McGee
- Re: [AMBER] How can I use FF14SB in DOCK6 calculation? (Thu Apr 28 2016 - 06:53:43 PDT)
- Re: [AMBER] Problem Running MMPBSA.py (Mon Apr 25 2016 - 21:41:20 PDT)
Eiros Zamora, Juan
- [AMBER] [cpptraj] Automating pcmin/pcmax selection of modes command (Tue Apr 19 2016 - 04:52:01 PDT)
- Re: [AMBER] Periodicity box (Fri Apr 01 2016 - 02:21:15 PDT)
Elisa Pieri
- [AMBER] How to rebuild pH-based trajectory files from CpHMD restarted simulations (Mon Apr 25 2016 - 02:39:46 PDT)
- [AMBER] Approach for transmembrane protein (Tue Apr 19 2016 - 05:03:53 PDT)
Elvis Martis
- Re: [AMBER] Regarding atom types (Fri Apr 22 2016 - 07:08:00 PDT)
- [AMBER] Regarding atom types (Tue Apr 19 2016 - 21:56:47 PDT)
Francisco Corzana López
- Re: [AMBER] Problems running MD simulation using residual dipolar couplings as restraints (Fri Apr 01 2016 - 08:13:01 PDT)
- [AMBER] Problems running MD simulation using residual dipolar couplings as restraints (Thu Mar 31 2016 - 23:31:35 PDT)
FyD
- Re: [AMBER] Problem with MCPB.py (Sat Apr 09 2016 - 01:28:41 PDT)
- Re: [AMBER] Metal geometry (Sat Apr 09 2016 - 01:19:01 PDT)
- Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 (Sat Apr 09 2016 - 01:10:52 PDT)
- Re: [AMBER] Run Stage 2 of the RESP fit (Wed Apr 06 2016 - 06:50:27 PDT)
Gard Nelson
- [AMBER] mpi problems (Mon Apr 18 2016 - 11:46:06 PDT)
giulia palermo
- Re: [AMBER] accelerated MD on set of dihedrals (Fri Apr 29 2016 - 11:47:21 PDT)
- [AMBER] rotation angle around an axes (Mon Apr 25 2016 - 10:55:54 PDT)
- Re: [AMBER] building DNA with extruded base (Tue Apr 19 2016 - 13:50:12 PDT)
- [AMBER] building DNA with extruded base (Tue Apr 19 2016 - 10:17:46 PDT)
Giuseppina La Sala
- Re: [AMBER] accelerated MD on set of dihedrals (Fri Apr 29 2016 - 15:15:52 PDT)
- Re: [AMBER] accelerated MD on set of dihedrals (Fri Apr 29 2016 - 15:14:06 PDT)
- [AMBER] accelerated MD on set of dihedrals (Fri Apr 29 2016 - 09:56:00 PDT)
Gould, Ian R
- Re: [AMBER] sander number of atoms limit (Tue Apr 05 2016 - 02:30:44 PDT)
- Re: [AMBER] sander number of atoms limit (Tue Apr 05 2016 - 02:27:26 PDT)
- Re: [AMBER] sander number of atoms limit (Tue Apr 05 2016 - 02:12:54 PDT)
Gustavo Seabra
- Re: [AMBER] Convergence problem with the SCC-DFTB example. (Wed Apr 06 2016 - 07:21:29 PDT)
- Re: [AMBER] QM calculation (Tue Apr 05 2016 - 13:06:51 PDT)
Hai Nguyen
- Re: [AMBER] interactive MD applied to AI (Thu Apr 21 2016 - 19:59:10 PDT)
- Re: [AMBER] interactive MD applied to AI (Thu Apr 21 2016 - 18:17:39 PDT)
- Re: [AMBER] amber v16 (Mon Apr 18 2016 - 12:43:04 PDT)
- Re: [AMBER] hbond analysis of phosphotyrosine (Thu Apr 14 2016 - 23:48:38 PDT)
- Re: [AMBER] Protein-DNA docking (Tue Apr 12 2016 - 13:51:07 PDT)
- Re: [AMBER] CHAMBER error for the updated CHARMM36 force fields (Tue Apr 12 2016 - 09:23:37 PDT)
- Re: [AMBER] CHAMBER and CMAP error using new c36 FF (Tue Apr 12 2016 - 07:34:02 PDT)
- Re: [AMBER] Implicit Solvent simulation - membrane proteins (Mon Apr 11 2016 - 10:58:51 PDT)
- Re: [AMBER] geometric center with cpptraj (Mon Apr 11 2016 - 07:01:05 PDT)
- Re: [AMBER] running charmm force field in amber (Wed Apr 06 2016 - 17:47:55 PDT)
Hannes Loeffler
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Thu Apr 21 2016 - 05:46:24 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Thu Apr 21 2016 - 03:13:49 PDT)
- Re: [AMBER] TI Calculation doubt (Sat Apr 16 2016 - 01:18:23 PDT)
hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Cpptraj LipidOrder error: mask groups are not the same length (Thu Apr 28 2016 - 12:10:55 PDT)
- Re: [AMBER] Cpptraj LipidOrder error: mask groups are not the same length (Thu Apr 28 2016 - 12:06:04 PDT)
- Re: [AMBER] on antechamber (Sun Apr 17 2016 - 23:49:59 PDT)
- Re: [AMBER] General question (Mon Apr 04 2016 - 05:27:05 PDT)
- Re: [AMBER] General question (Mon Apr 04 2016 - 03:57:40 PDT)
- Re: [AMBER] General question (Mon Apr 04 2016 - 03:17:38 PDT)
- Re: [AMBER] General question (Mon Apr 04 2016 - 00:08:57 PDT)
- Re: [AMBER] General question (Sun Apr 03 2016 - 23:21:12 PDT)
- Re: [AMBER] How to use tiMerge properly in pmemd TI calculation (Sun Apr 03 2016 - 07:03:23 PDT)
- Re: [AMBER] How to use tiMerge properly in pmemd TI calculation (Sun Apr 03 2016 - 06:41:22 PDT)
Harmeet Kaur
- [AMBER] error while running MMPBSA script (Mon Apr 11 2016 - 21:52:12 PDT)
Jag Silwal
- [AMBER] Calculate Percentage of Hydrogen Occurrence (Fri Apr 29 2016 - 06:27:54 PDT)
- [AMBER] Decomposition energy after mutation! (Fri Apr 22 2016 - 09:52:14 PDT)
- Re: [AMBER] Change PBRadii after simulation (Mon Apr 18 2016 - 05:50:14 PDT)
- Re: [AMBER] Change PBRadii after simulation (Sat Apr 16 2016 - 21:20:37 PDT)
- [AMBER] Change PBRadii after simulation (Sat Apr 16 2016 - 20:30:27 PDT)
- Re: [AMBER] Alanine Scanning ERROR!!! (Thu Apr 14 2016 - 04:46:49 PDT)
- Re: [AMBER] Alanine Scanning ERROR!!! (Wed Apr 13 2016 - 15:22:39 PDT)
- [AMBER] Alanine Scanning ERROR!!! (Mon Apr 11 2016 - 19:11:17 PDT)
James Starlight
- Re: [AMBER] tleap parametrization of metalo-binding proteins (Wed Apr 27 2016 - 07:01:05 PDT)
- Re: [AMBER] tleap parametrization of metalo-binding proteins (Wed Apr 27 2016 - 05:54:55 PDT)
- [AMBER] tleap parametrization of metalo-binding proteins (Wed Apr 27 2016 - 02:25:23 PDT)
- [AMBER] MD tutorial workflows (Mon Apr 11 2016 - 01:36:35 PDT)
Jason Swails
- Re: [AMBER] mmpbsa complex (Fri Apr 29 2016 - 18:46:45 PDT)
- Re: [AMBER] ambpdb error (Fri Apr 29 2016 - 10:22:33 PDT)
- Re: [AMBER] ambpdb error (Fri Apr 29 2016 - 08:59:13 PDT)
- Re: [AMBER] Problem Running MMPBSA.py (Tue Apr 26 2016 - 05:45:06 PDT)
- Re: [AMBER] Read/visualize volmap output (opendx) (Mon Apr 25 2016 - 05:53:40 PDT)
- Re: [AMBER] How to rebuild pH-based trajectory files from CpHMD restarted simulations (Mon Apr 25 2016 - 03:16:18 PDT)
- Re: [AMBER] Read/visualize volmap output (opendx) (Mon Apr 25 2016 - 03:14:01 PDT)
- Re: [AMBER] Decomposition energy after mutation! (Sat Apr 23 2016 - 21:58:51 PDT)
- Re: [AMBER] mmpbsa complex (Thu Apr 21 2016 - 19:12:53 PDT)
- Re: [AMBER] qmmm mmpbsa spin multiplicity problem (Thu Apr 21 2016 - 10:02:04 PDT)
- Re: [AMBER] Electrostatic Energies - MMPBSA (Wed Apr 20 2016 - 11:30:55 PDT)
- Re: [AMBER] Electrostatic Energies - MMPBSA (Tue Apr 19 2016 - 18:36:24 PDT)
- Re: [AMBER] how to embed amber14 (Mon Apr 18 2016 - 03:54:09 PDT)
- Re: [AMBER] how to embed amber14 (Sun Apr 17 2016 - 09:27:03 PDT)
- Re: [AMBER] Change PBRadii after simulation (Sun Apr 17 2016 - 08:00:52 PDT)
- Re: [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file (Fri Apr 15 2016 - 13:07:54 PDT)
- Re: [AMBER] Amber custom hardware setup (Wed Apr 13 2016 - 19:05:44 PDT)
- Re: [AMBER] Alanine Scanning ERROR!!! (Wed Apr 13 2016 - 19:01:46 PDT)
- Re: [AMBER] Alanine Scanning ERROR!!! (Wed Apr 13 2016 - 09:53:29 PDT)
- Re: [AMBER] MMGBSA and dielectric constants (Wed Apr 13 2016 - 09:49:58 PDT)
- Re: [AMBER] CHAMBER and CMAP error using new c36 FF (Wed Apr 13 2016 - 03:33:11 PDT)
- Re: [AMBER] CHAMBER and CMAP error using new c36 FF (Tue Apr 12 2016 - 07:27:38 PDT)
- Re: [AMBER] error while running MMPBSA script (Tue Apr 12 2016 - 07:07:26 PDT)
- Re: [AMBER] Is it possible to run TI with pmemd using the AMOEBA force field? (Sun Apr 10 2016 - 17:13:27 PDT)
- Re: [AMBER] Error -per residue Energy Decomposition (Fri Apr 08 2016 - 18:39:45 PDT)
- Re: [AMBER] Regarding MM-PBSA free energy calculation (Fri Apr 08 2016 - 05:13:57 PDT)
- Re: [AMBER] Regarding MM-PBSA calculation (Fri Apr 08 2016 - 05:12:32 PDT)
- Re: [AMBER] MMPBSA : Calculation when keeping explicit water molecules (Fri Apr 08 2016 - 05:11:17 PDT)
- Re: [AMBER] CpHMD (Fri Apr 08 2016 - 05:07:50 PDT)
- Re: [AMBER] test: not getting emails from the list (Thu Apr 07 2016 - 09:31:35 PDT)
- Re: [AMBER] Amber: .rst file not created (Thu Apr 07 2016 - 09:28:33 PDT)
- Re: [AMBER] running charmm force field in amber (Wed Apr 06 2016 - 18:05:18 PDT)
- Re: [AMBER] Amber14/AmberTools15 compliation error (Wed Apr 06 2016 - 07:42:00 PDT)
- Re: [AMBER] sander number of atoms limit (Tue Apr 05 2016 - 05:07:23 PDT)
- Re: [AMBER] turning of non-bonded interactions with addExclusions (Mon Apr 04 2016 - 09:10:09 PDT)
- Re: [AMBER] MD simulations of deprotonated tyrosine residue with AMBER (Mon Apr 04 2016 - 09:03:17 PDT)
- Re: [AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm (Mon Apr 04 2016 - 06:47:34 PDT)
- [AMBER] Introducing the exciting next step in MD software development (Fri Apr 01 2016 - 03:32:51 PDT)
Jean-Patrick Francoia
- Re: [AMBER] Read/visualize volmap output (opendx) (Mon Apr 25 2016 - 13:46:47 PDT)
- Re: [AMBER] Read/visualize volmap output (opendx) (Mon Apr 25 2016 - 12:26:08 PDT)
- Re: [AMBER] Read/visualize volmap output (opendx) (Mon Apr 25 2016 - 06:12:45 PDT)
- Re: [AMBER] Read/visualize volmap output (opendx) (Mon Apr 25 2016 - 03:54:13 PDT)
- [AMBER] Read/visualize volmap output (opendx) (Mon Apr 25 2016 - 01:44:54 PDT)
Jesmita Dhar
- Re: [AMBER] Could not find angle parameter (Mon Apr 11 2016 - 22:34:13 PDT)
- [AMBER] Could not find angle parameter (Mon Apr 11 2016 - 02:32:32 PDT)
jfliu.itcs.ecnu.edu.cn
- Re: [AMBER] How to use tiMerge properly in pmemd TI calculation (Sun Apr 03 2016 - 07:22:50 PDT)
- Re: [AMBER] How to use tiMerge properly in pmemd TI calculation (Sun Apr 03 2016 - 06:55:48 PDT)
- [AMBER] How to use tiMerge properly in pmemd TI calculation (Sun Apr 03 2016 - 06:29:11 PDT)
Jiaqi Jin
- [AMBER] Using PBSA to Calculate Solvation Free Energy (Mon Apr 25 2016 - 15:31:48 PDT)
jixiaofeng
- Re: [AMBER] atom does not have a type (Thu Apr 21 2016 - 19:31:45 PDT)
- [AMBER] atom does not have a type (Thu Apr 21 2016 - 19:23:53 PDT)
- [AMBER] was the MCPB.py compiled correctly？ (Sun Apr 17 2016 - 19:59:35 PDT)
- [AMBER] error in MCPB.py 3b (Sun Apr 17 2016 - 19:43:18 PDT)
Jun Feng
- Re: [AMBER] CHAMBER and CMAP error using new c36 FF (Tue Apr 12 2016 - 11:35:44 PDT)
- [AMBER] CHAMBER and CMAP error using new c36 FF (Tue Apr 12 2016 - 07:22:49 PDT)
- [AMBER] CHAMBER and CMAP error using new c36 FF (Mon Apr 11 2016 - 10:18:17 PDT)
Karolina Markowska
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Mon Apr 25 2016 - 05:00:08 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Sun Apr 24 2016 - 12:16:02 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Fri Apr 22 2016 - 02:24:26 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Thu Apr 21 2016 - 03:43:18 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? (Thu Apr 21 2016 - 03:11:56 PDT)
- [AMBER] How to read mdinfo file without crashing the simulation? (Thu Apr 21 2016 - 02:01:03 PDT)
Kasprzak, Wojciech (NIH/NCI) [C]
- [AMBER] System size limitations for Amber 14 pmemd.cuda? (Fri Apr 22 2016 - 05:48:38 PDT)
Kenneth McGuinness
- Re: [AMBER] Building Cyclic Peptide in xleap (Fri Apr 22 2016 - 09:43:36 PDT)
- Re: [AMBER] How can I extract PDB files from a molecular dynamics simulation (Thu Apr 14 2016 - 19:10:23 PDT)
- Re: [AMBER] Natural bond orbital analysis (Thu Apr 14 2016 - 13:06:53 PDT)
- [AMBER] Natural bond orbital analysis (Wed Apr 13 2016 - 07:31:40 PDT)
- Re: [AMBER] spherical restraint flatwell potentials (Mon Apr 04 2016 - 14:35:55 PDT)
- Re: [AMBER] spherical restraint flatwell potentials (Mon Apr 04 2016 - 11:52:26 PDT)
- [AMBER] spherical restraint flatwell potentials (Mon Apr 04 2016 - 11:03:05 PDT)
Krantzman, Kristin D
- [AMBER] Hbond command use with non-hydrogen bonds (Thu Apr 07 2016 - 07:49:56 PDT)
Kris Feher
- Re: [AMBER] Amber14/AmberTools15 compliation error (Tue Apr 12 2016 - 01:19:19 PDT)
- [AMBER] Amber14/AmberTools15 compliation error (Wed Apr 06 2016 - 07:34:04 PDT)
kurisaki
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion (Thu Apr 21 2016 - 18:57:39 PDT)
Lachele Foley
- Re: [AMBER] glycam O-glycosylation at Ser (Mon Apr 18 2016 - 23:59:06 PDT)
- Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 (Fri Apr 08 2016 - 21:29:02 PDT)
- Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 (Fri Apr 08 2016 - 20:07:24 PDT)
Lara rajam
- Re: [AMBER] Protein-DNA docking (Tue Apr 12 2016 - 13:56:02 PDT)
- [AMBER] Protein-DNA docking (Tue Apr 12 2016 - 13:38:40 PDT)
Leonardo Lazzaro
- [AMBER] Amber custom hardware setup (Wed Apr 13 2016 - 17:39:55 PDT)
Lorenzo Gontrani
- Re: [AMBER] Question about RESP with iodine (Wed Apr 27 2016 - 06:50:53 PDT)
- [AMBER] Question about RESP with iodine (Wed Apr 27 2016 - 03:55:29 PDT)
Luis Esteban
- Re: [AMBER] How can I extract PDB files from a molecular dynamics simulation (Sat Apr 16 2016 - 17:29:07 PDT)
- Re: [AMBER] How can I extract PDB files from a molecular dynamics simulation (Thu Apr 14 2016 - 19:39:01 PDT)
- [AMBER] How can I extract PDB files from a molecular dynamics simulation (Thu Apr 14 2016 - 19:02:03 PDT)
Luke Presson
- Re: [AMBER] Problems with periodic boundaries (Fri Apr 01 2016 - 13:27:53 PDT)
- Re: [AMBER] Problems with periodic boundaries (Fri Apr 01 2016 - 12:37:01 PDT)
- [AMBER] Problems with periodic boundaries (Fri Apr 01 2016 - 06:24:53 PDT)
Maral Aminpour
- Re: [AMBER] Building Cyclic Peptide in xleap (Thu Apr 28 2016 - 08:15:02 PDT)
- [AMBER] Building Cyclic Peptide in xleap (Thu Apr 21 2016 - 13:55:19 PDT)
Marc van der Kamp
- Re: [AMBER] How can I use FF14SB in DOCK6 calculation? (Fri Apr 29 2016 - 01:09:37 PDT)
- Re: [AMBER] error while putting the whole path into python script (Wed Apr 20 2016 - 00:51:13 PDT)
- Re: [AMBER] QM calculation (Tue Apr 05 2016 - 14:31:24 PDT)
Marcelo Andrade Chagas
- Re: [AMBER] mpi problems (Mon Apr 18 2016 - 12:16:22 PDT)
- Re: [AMBER] Amber script to delete all hydrogen atoms from protein? (Sun Apr 10 2016 - 04:05:38 PDT)
- Re: [AMBER] Amber: .rst file not created (Wed Apr 06 2016 - 07:42:30 PDT)
Marek Maly
- Re: [AMBER] GeForce GTX 960 ? (Thu Apr 21 2016 - 15:36:45 PDT)
- [AMBER] GeForce GTX 960 ? (Thu Apr 21 2016 - 08:51:43 PDT)
Martin Floor
- [AMBER] Problem Running MMPBSA.py (Mon Apr 25 2016 - 15:29:23 PDT)
Martina Devi
- Re: [AMBER] hoogsteen base pair (Fri Apr 01 2016 - 08:25:28 PDT)
- [AMBER] hoogsteen base pair (Fri Apr 01 2016 - 08:23:48 PDT)
Mary Varughese
- [AMBER] TI Calculation doubt (Fri Apr 15 2016 - 23:34:02 PDT)
McElheny, Dan
- Re: [AMBER] mmpbsa complex (Fri Apr 29 2016 - 13:57:42 PDT)
- [AMBER] mmpbsa complex (Thu Apr 21 2016 - 12:42:52 PDT)
Michael Shokhen
- Re: [AMBER] Amber script to delete all hydrogen atoms from protein? (Sun Apr 10 2016 - 05:25:45 PDT)
- [AMBER] Amber script to delete all hydrogen atoms from protein? (Sun Apr 10 2016 - 02:11:18 PDT)
- [AMBER] aMD ruins membrane structure (Fri Apr 01 2016 - 01:03:06 PDT)
Mijiddorj Batsaikhan
- Re: [AMBER] How can I use FF14SB in DOCK6 calculation? (Thu Apr 28 2016 - 22:03:55 PDT)
- [AMBER] How can I use FF14SB in DOCK6 calculation? (Thu Apr 28 2016 - 03:20:40 PDT)
- [AMBER] Hydroxyproline (Sat Apr 23 2016 - 05:00:41 PDT)
- Re: [AMBER] how to prepare a pdb file of a protein being phosphorylated at specific residues (Sun Apr 03 2016 - 21:53:13 PDT)
- Re: [AMBER] how to run a MD of a phosphorylated protein using amber (Sun Apr 03 2016 - 21:30:28 PDT)
- Re: [AMBER] Hydrophobic solution environment ??? (Sat Apr 02 2016 - 01:50:43 PDT)
mohammad r
- Re: [AMBER] QM calculation (Fri Apr 08 2016 - 02:12:24 PDT)
- Re: [AMBER] QM calculation (Mon Apr 04 2016 - 12:06:04 PDT)
- Re: [AMBER] QM calculation (Sun Apr 03 2016 - 11:20:49 PDT)
- Re: [AMBER] QM calculation (Sun Apr 03 2016 - 03:48:04 PDT)
- [AMBER] QM calculation (Fri Apr 01 2016 - 22:54:34 PDT)
Neal Broomhead
- [AMBER] LEAP RUN FAILED (Thu Apr 14 2016 - 02:38:06 PDT)
Neha Gandhi
- Re: [AMBER] glycam O-glycosylation at Ser (Tue Apr 19 2016 - 00:16:46 PDT)
- [AMBER] glycam O-glycosylation at Ser (Mon Apr 18 2016 - 22:17:43 PDT)
- Re: [AMBER] running charmm force field in amber (Wed Apr 06 2016 - 18:40:52 PDT)
- [AMBER] running charmm force field in amber (Wed Apr 06 2016 - 17:37:56 PDT)
Niharikav Veeresh
- Re: [AMBER] AMBER Project (Tue Apr 26 2016 - 11:52:30 PDT)
Nikolay N. Kuzmich
- Re: [AMBER] XLeap didn't save the parameter file (Fri Apr 22 2016 - 05:39:11 PDT)
- [AMBER] XLeap didn't save the parameter file (Wed Apr 20 2016 - 01:27:17 PDT)
Pengfei Li
- Re: [AMBER] tleap parametrization of metalo-binding proteins (Thu Apr 28 2016 - 07:51:29 PDT)
- Re: [AMBER] tleap parametrization of metalo-binding proteins (Wed Apr 27 2016 - 06:53:03 PDT)
- Re: [AMBER] Question about RESP with iodine (Wed Apr 27 2016 - 06:39:37 PDT)
- Re: [AMBER] Metal geometry (Mon Apr 11 2016 - 20:11:44 PDT)
- Re: [AMBER] Metal geometry (Sat Apr 09 2016 - 19:42:44 PDT)
- Re: [AMBER] Metal geometry (Sat Apr 09 2016 - 07:29:15 PDT)
peter.schmidtke.discngine.servier.com
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj (Wed Apr 20 2016 - 05:30:27 PDT)
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj (Wed Apr 20 2016 - 01:27:25 PDT)
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj (Tue Apr 19 2016 - 08:23:13 PDT)
- [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj (Tue Apr 19 2016 - 05:41:14 PDT)
Prayagraj Fandilolu
- Re: [AMBER] No torsion terms for CB-N*-CR-H5 (Wed Apr 27 2016 - 23:29:11 PDT)
- [AMBER] No torsion terms for CB-N*-CR-H5 (Sun Apr 24 2016 - 00:12:13 PDT)
Ray Luo
- Re: [AMBER] Using PBSA to Calculate Solvation Free Energy (Mon Apr 25 2016 - 15:56:49 PDT)
- Re: [AMBER] Implicit Solvent simulation - membrane proteins (Mon Apr 11 2016 - 11:21:47 PDT)
- Re: [AMBER] mm_pbsa.pl, that I'm doing this right? (Mon Apr 11 2016 - 08:25:21 PDT)
Robert Molt
- [AMBER] General Type Improper Dihedrals vs. Specifics (Wed Apr 06 2016 - 14:20:15 PDT)
Ross Walker
- Re: [AMBER] CUDA and restraint (Fri Apr 29 2016 - 08:28:42 PDT)
- Re: [AMBER] GeForce GTX 960 ? (Mon Apr 25 2016 - 08:20:44 PDT)
- Re: [AMBER] GeForce GTX 960 ? (Thu Apr 21 2016 - 10:18:30 PDT)
- Re: [AMBER] running charmm force field in amber (Wed Apr 06 2016 - 17:50:23 PDT)
Saheb Dutta
- [AMBER] Problem in calculating auto time correlation function with ptraj (Wed Apr 27 2016 - 08:32:55 PDT)
Saman Yousuf ali
- [AMBER] MD of 1:1 mixture compound (Tue Apr 26 2016 - 22:10:56 PDT)
- Re: [AMBER] cpptraj SolventAcc and ligand distance plotting (Thu Apr 21 2016 - 14:17:40 PDT)
- [AMBER] cpptraj SolventAcc and ligand distance plotting (Sat Apr 16 2016 - 23:59:11 PDT)
- [AMBER] query regarding dssp plot cpptraj. (Sat Apr 09 2016 - 08:20:18 PDT)
Sanjib Paul
- [AMBER] parmed.py (Tue Apr 26 2016 - 07:44:15 PDT)
Scott Brozell
- Re: [AMBER] tleap - protein + ligand + heme group (Thu Apr 28 2016 - 10:35:26 PDT)
Shreeramesh
- [AMBER] Error while converting CHARMM-GUI generated file (Mon Apr 25 2016 - 05:17:08 PDT)
- [AMBER] Error in the conversion of CHARMM-GUI generated file into lipid14 readable format (Thu Apr 21 2016 - 00:52:48 PDT)
- Re: [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file (Fri Apr 15 2016 - 05:16:18 PDT)
- [AMBER] Conversion of CHARMM-GUI generated file into Lipid14 readable file (Fri Apr 15 2016 - 05:01:04 PDT)
- [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file (Fri Apr 15 2016 - 04:27:48 PDT)
Shukla, Saurabh
- [AMBER] Targeted MD error (Thu Apr 28 2016 - 09:46:03 PDT)
Sivanandam M
- [AMBER] Regarding Input file preparation in AMBER (Thu Apr 14 2016 - 00:01:41 PDT)
- [AMBER] Regarding MM-PBSA free energy calculation (Fri Apr 08 2016 - 03:51:05 PDT)
- [AMBER] Regarding MM-PBSA calculation (Fri Apr 08 2016 - 03:44:33 PDT)
Sofia Vasilakaki
- [AMBER] PCA (Thu Apr 07 2016 - 11:59:38 PDT)
Sreemol G
- Re: [AMBER] RMSD graph for protein-RNA complex (Tue Apr 12 2016 - 22:16:10 PDT)
- Re: [AMBER] RMSD graph for protein-RNA complex (Tue Apr 12 2016 - 22:06:57 PDT)
- Re: [AMBER] RMSD graph for protein-RNA complex (Tue Apr 12 2016 - 05:13:42 PDT)
- Re: [AMBER] RMSD graph for protein-RNA complex (Mon Apr 11 2016 - 22:07:55 PDT)
- Re: [AMBER] RMSD graph for protein-RNA complex (Fri Apr 08 2016 - 04:04:35 PDT)
- [AMBER] RMSD graph for protein-RNA complex (Fri Apr 08 2016 - 01:15:07 PDT)
- Re: [AMBER] General question (Tue Apr 05 2016 - 22:42:48 PDT)
- Re: [AMBER] General question (Tue Apr 05 2016 - 21:31:13 PDT)
- Re: [AMBER] General question (Mon Apr 04 2016 - 04:35:01 PDT)
- Re: [AMBER] General question (Mon Apr 04 2016 - 03:39:24 PDT)
- Re: [AMBER] General question (Mon Apr 04 2016 - 02:57:41 PDT)
- Re: [AMBER] General question (Sun Apr 03 2016 - 23:47:58 PDT)
- [AMBER] General question (Sun Apr 03 2016 - 23:04:28 PDT)
Stevens, David Ryan
- Re: [AMBER] Multiple restraints for minimization (Mon Apr 11 2016 - 14:25:07 PDT)
- Re: [AMBER] Multiple restraints for minimization (Mon Apr 11 2016 - 11:56:29 PDT)
- [AMBER] Multiple restraints for minimization (Mon Apr 11 2016 - 09:03:08 PDT)
Sumsamber Lee
- [AMBER] Is it possible to run TI with pmemd using the AMOEBA force field? (Sun Apr 10 2016 - 15:07:03 PDT)
sunita gupta
- Re: [AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm (Mon Apr 04 2016 - 05:17:32 PDT)
- [AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm (Thu Mar 31 2016 - 23:22:59 PDT)
Surya Prakash Tiwari
- [AMBER] Problem with MCPB.py (Fri Apr 08 2016 - 11:09:32 PDT)
Takuya Uto
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion (Mon Apr 25 2016 - 03:50:16 PDT)
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion (Sat Apr 23 2016 - 02:49:22 PDT)
- [AMBER] How to deal with monoatomic ion, such as ILs anion (Thu Apr 21 2016 - 18:45:45 PDT)
- [AMBER] How to deal with monoatomic ion, such as ILs cation (Thu Apr 21 2016 - 18:29:56 PDT)
TERREUX RAPHAEL
- Re: [AMBER] sander number of atoms limit (Tue Apr 05 2016 - 02:16:04 PDT)
- [AMBER] sander number of atoms limit (Tue Apr 05 2016 - 01:59:59 PDT)
Thomas Pochapsky
- Re: [AMBER] Introducing the exciting next step in MD software development (Fri Apr 01 2016 - 05:48:59 PDT)
Tyler Luchko (Lists)
- Re: [AMBER] Error in 3DRISM calculation (Sun Apr 17 2016 - 22:51:08 PDT)
Vasantha Kumar
- Re: [AMBER] Refinement in explicit solvent (Mon Apr 11 2016 - 16:30:22 PDT)
- [AMBER] Refinement in explicit solvent (Mon Apr 11 2016 - 01:13:19 PDT)
- Re: [AMBER] Metal geometry (Sun Apr 10 2016 - 06:40:34 PDT)
- Re: [AMBER] Metal geometry (Sat Apr 09 2016 - 04:20:27 PDT)
- Re: [AMBER] Metal geometry (Fri Apr 08 2016 - 16:42:04 PDT)
- Re: [AMBER] Metal geometry (Fri Apr 08 2016 - 16:29:14 PDT)
- [AMBER] Metal geometry (Fri Apr 08 2016 - 06:13:15 PDT)
Vlad Cojocaru
- [AMBER] Early bird extended! ISQBP2016 meeting - Bergen Norway (Mon Apr 18 2016 - 12:34:15 PDT)
- [AMBER] test: not getting emails from the list (Thu Apr 07 2016 - 01:24:04 PDT)
- [AMBER] cpptraj: reading in previously created covariance matrix (Wed Apr 06 2016 - 01:09:16 PDT)
- [AMBER] cpptraj: reading in previously created covariance matrix (Tue Apr 05 2016 - 12:52:57 PDT)
waleed zalloum
- [AMBER] clustering (Mon Apr 18 2016 - 11:14:33 PDT)
wjli
- Re: [AMBER] ff12SB force field (Mon Apr 11 2016 - 07:02:23 PDT)
- [AMBER] ff12SB force field (Mon Apr 11 2016 - 06:47:05 PDT)
- [AMBER] PMF calculation via tunnel (SMD) (Sun Apr 10 2016 - 05:03:23 PDT)
- [AMBER] 回复： The question about SMD (Tue Apr 05 2016 - 18:08:36 PDT)
- [AMBER] 回复： The question about SMD (Tue Apr 05 2016 - 18:01:39 PDT)
- [AMBER] The question about SMD (Tue Apr 05 2016 - 06:56:05 PDT)
Wu Xu
- Re: [AMBER] hbond analysis of phosphotyrosine (Sat Apr 16 2016 - 09:41:32 PDT)
- Re: [AMBER] hbond analysis of phosphotyrosine (Fri Apr 15 2016 - 10:09:41 PDT)
- Re: [AMBER] hbond analysis of phosphotyrosine (Fri Apr 15 2016 - 05:13:13 PDT)
- [AMBER] hbond analysis of phosphotyrosine (Thu Apr 14 2016 - 19:55:56 PDT)
YanhuaOuyang
- Re: [AMBER] build a phosphorylated protein structure pdb file (Tue Apr 05 2016 - 04:58:21 PDT)
- Re: [AMBER] build a phosphorylated protein structure pdb file (Mon Apr 04 2016 - 18:25:46 PDT)
- Re: [AMBER] build a phosphorylated protein structure pdb file (Mon Apr 04 2016 - 18:04:40 PDT)
- [AMBER] build a phosphorylated protein structure pdb file (Mon Apr 04 2016 - 00:21:29 PDT)
- Re: [AMBER] how to prepare a pdb file of a protein being phosphorylated at specific residues (Mon Apr 04 2016 - 00:06:29 PDT)
- Re: [AMBER] how to run a MD of a phosphorylated protein using amber (Sun Apr 03 2016 - 23:46:28 PDT)
yhzahsc
- [AMBER] mm_pbsa.pl ERROR (Thu Apr 14 2016 - 00:42:02 PDT)
- [AMBER] Run Stage 2 of the RESP fit (Sun Apr 03 2016 - 00:17:13 PDT)
yhzahsc
- Re: [AMBER] mm_pbsa.pl ERROR (Thu Apr 14 2016 - 19:26:46 PDT)
- Re: [AMBER] mm_pbsa.pl ERROR (Thu Apr 14 2016 - 19:25:59 PDT)
- Re: [AMBER] Run Stage 2 of the RESP fit (Sun Apr 03 2016 - 17:35:20 PDT)
Yigal Lahav
- Re: [AMBER] tleap parametrization of metalo-binding proteins (Wed Apr 27 2016 - 04:07:26 PDT)
yuandandan
- [AMBER] questions about energy terms of amber MD (Wed Apr 20 2016 - 06:57:38 PDT)
Zhenyu Meng
- Re: [AMBER] debug issue (Thu Apr 28 2016 - 02:46:49 PDT)
- Re: [AMBER] debug issue (Wed Apr 27 2016 - 20:32:44 PDT)
- [AMBER] debug issue (Tue Apr 26 2016 - 23:53:13 PDT)
楊承翰
- [AMBER] MMPBSA : Calculation when keeping explicit water molecules (Thu Apr 07 2016 - 21:14:59 PDT)
欧阳艳华
- [AMBER] how to run a MD of a phosphorylated protein using amber (Sun Apr 03 2016 - 20:21:43 PDT)
- [AMBER] how to prepare a pdb file of a protein being phosphorylated at specific residues (Sun Apr 03 2016 - 20:15:03 PDT)
王美婷
- [AMBER] Energies in QM/MM MD (Mon Apr 25 2016 - 01:46:48 PDT)
赵聪
- [AMBER] CpHMD (Fri Apr 08 2016 - 01:17:00 PDT)
達南杰
- Re: [AMBER] Box dimensions (Mon Apr 11 2016 - 20:18:20 PDT)
- Re: [AMBER] Box dimensions (Mon Apr 11 2016 - 19:36:17 PDT)
- [AMBER] Box dimensions (Mon Apr 11 2016 - 04:28:21 PDT)

Amber Archive Apr 2016 by author