Amber Archive May 2019: by author

Abhilash J
- Re: [AMBER] Temperature variation in QM/MM simulation with AMBER18/G09 (Fri May 24 2019 - 22:53:38 PDT)
- [AMBER] Temperature variation in QM/MM simulation with AMBER18/G09 (Wed May 22 2019 - 11:38:05 PDT)
Abhishek Sirohiwal
- Re: [AMBER] Protein-Lipid Bilayer PDB preparation Issue(s) (Mon May 27 2019 - 11:31:10 PDT)
- [AMBER] Protein-Lipid Bilayer PDB preparation Issue(s) (Mon May 27 2019 - 09:48:32 PDT)
Akshay Prabhakant
- Re: [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 (Tue May 14 2019 - 03:03:12 PDT)
- Re: [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 (Mon May 13 2019 - 07:01:26 PDT)
- [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 (Mon May 13 2019 - 06:53:49 PDT)
- [AMBER] pmemd.cuda "cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered" (Wed May 08 2019 - 08:50:21 PDT)
- Re: [AMBER] matching energies betwen amber-md and gromacs using amber parameters in both (Mon May 06 2019 - 04:11:58 PDT)
- [AMBER] matching energies betwen amber-md and gromacs using amber parameters in both (Mon May 06 2019 - 02:59:06 PDT)
- [AMBER] umbrella sampling using pmemd in amber/2016 (Sun May 05 2019 - 08:30:04 PDT)
- [AMBER] check version (Sun May 05 2019 - 05:29:29 PDT)
Albert
- Re: [AMBER] anybody has any idea? (Thu May 30 2019 - 04:14:51 PDT)
- [AMBER] anybody has any idea? (Thu May 30 2019 - 00:17:35 PDT)
- [AMBER] problem of srun (Wed May 29 2019 - 05:51:46 PDT)
Alessandro Contini
- Re: [AMBER] Capping a dipeptide with Boc (Wed May 08 2019 - 09:29:09 PDT)
- Re: [AMBER] Capping a dipeptide with Boc (Wed May 08 2019 - 07:33:38 PDT)
- Re: [AMBER] Capping a dipeptide with Boc (Wed May 08 2019 - 04:14:46 PDT)
Alessandro LANDI
- [AMBER] Using a box of organic solvent (Fri May 31 2019 - 03:42:08 PDT)
ali akbar
- [AMBER] running qsub files in a single standalone workstation (Tue May 07 2019 - 22:32:49 PDT)
- Re: [AMBER] AMBER Digest, Vol 2638, Issue 1 (Tue May 07 2019 - 22:07:54 PDT)
- [AMBER] running qsub files in a single standalone workstation (Tue May 07 2019 - 03:28:21 PDT)
- [AMBER] FEW- an issue generating *.lib for ligand (Sat May 04 2019 - 00:39:44 PDT)
- [AMBER] FEW not producing *.lib file for ligand (Thu May 02 2019 - 02:50:12 PDT)
anu chandra
- Re: [AMBER] CPPTRAJ average residue-wise contact map (Thu May 02 2019 - 08:30:48 PDT)
- [AMBER] CPPTRAJ average residue-wise contact map (Wed May 01 2019 - 12:06:24 PDT)
Batuhan Kav
- [AMBER] different energy values from mdout and cpptraj (Tue May 07 2019 - 05:24:18 PDT)
Beale, John
- [AMBER] Vina Zinc (Wed May 01 2019 - 04:05:56 PDT)
Bill Ross
- Re: [AMBER] Optimization of geometry in xleap (Wed May 29 2019 - 23:36:14 PDT)
- Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 (Wed May 29 2019 - 12:09:53 PDT)
- Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 (Wed May 29 2019 - 07:12:15 PDT)
- Re: [AMBER] How to generate the correct force field parameter for a large molecule? (Mon May 27 2019 - 00:52:02 PDT)
- Re: [AMBER] RMSF of combined trajectory (Thu May 16 2019 - 23:17:31 PDT)
- Re: [AMBER] RMSF of combined trajectory (Thu May 16 2019 - 23:16:02 PDT)
- Re: [AMBER] RMSF of combined trajectory (Thu May 16 2019 - 04:59:21 PDT)
- Re: [AMBER] Bubbles during NPT and NVT simulations (Thu May 16 2019 - 03:13:54 PDT)
- Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file (Thu May 16 2019 - 03:03:55 PDT)
- Re: [AMBER] Average structure vs Individual frames (Mon May 13 2019 - 19:53:18 PDT)
- Re: [AMBER] Average structure vs Individual frames (Mon May 13 2019 - 18:50:15 PDT)
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid (Mon May 13 2019 - 01:05:59 PDT)
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid (Mon May 13 2019 - 00:56:07 PDT)
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid (Sun May 12 2019 - 01:52:59 PDT)
- Re: [AMBER] Fwd: The unperturbed charge of the unit: 4.003000 is not zero (Sat May 11 2019 - 12:36:57 PDT)
Bouibes Amine
- [AMBER] Print Hessian matrix in (3,3) dimension (Sun May 26 2019 - 01:03:55 PDT)
Carlos Simmerling
- Re: [AMBER] Minimization input (Wed May 29 2019 - 03:47:35 PDT)
- Re: [AMBER] Bubbles during NPT and NVT simulations (Thu May 16 2019 - 03:02:03 PDT)
- [AMBER] Fwd: August 5-8.SBU: 2019 Summer School Parallel Computing in Molecular Sciences (Fri May 10 2019 - 07:09:40 PDT)
- Re: [AMBER] Unequal distribution of water (Tue May 07 2019 - 15:41:04 PDT)
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] (Sun May 05 2019 - 03:57:32 PDT)
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] (Sat May 04 2019 - 03:39:42 PDT)
- Re: [AMBER] Guidance on WHAM (Fri May 03 2019 - 08:14:49 PDT)
- Re: [AMBER] Novel Force Field Parameters for Aromatic Dihedrals (Thu May 02 2019 - 09:36:00 PDT)
Charles Lin
- Re: [AMBER] Simulating Water Exchange to Buried Binding Sites (Mon May 20 2019 - 10:10:56 PDT)
- Re: [AMBER] Simulating Water Exchange to Buried Binding Sites (Mon May 20 2019 - 10:09:22 PDT)
- Re: [AMBER] Simulating Water Exchange to Buried Binding Sites (Fri May 17 2019 - 10:45:25 PDT)
- Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file (Thu May 16 2019 - 08:06:50 PDT)
Charo del Genio
- Re: [AMBER] Question about sander running parallel (Fri May 31 2019 - 12:19:27 PDT)
- Re: [AMBER] Random segfaults (invalid memory reference) in sander (Wed May 15 2019 - 08:45:27 PDT)
- Re: [AMBER] Random segfaults (invalid memory reference) in sander (Mon May 06 2019 - 02:37:34 PDT)
- Re: [AMBER] Random segfaults (invalid memory reference) in sander (Fri May 03 2019 - 07:08:31 PDT)
- Re: [AMBER] Random segfaults (invalid memory reference) in sander (Thu May 02 2019 - 10:51:31 PDT)
- [AMBER] Random segfaults (invalid memory reference) in sander (Thu May 02 2019 - 01:43:19 PDT)
Charu Sharma (JRF)
- [AMBER] graph (Mon May 27 2019 - 04:06:01 PDT)
Chem Jubilant
- [AMBER] SMD using contact number (Wed May 01 2019 - 07:40:46 PDT)
Chris Neale
- Re: [AMBER] PCA with a really giant trajectory (Mon May 27 2019 - 00:29:24 PDT)
Cruzeiro,Vinicius Wilian D
- Re: [AMBER] empty cein file redox potential calculations (Thu May 30 2019 - 12:29:15 PDT)
- Re: [AMBER] Question regarding compatibility of Temperature replica exchange MD (TREMD) with constant pH MD (Fri May 03 2019 - 12:14:45 PDT)
Daniel Fernández Remacha
- Re: [AMBER] Guidance on WHAM (Tue May 07 2019 - 11:46:45 PDT)
Daniel Roe
- Re: [AMBER] Radgyr or distance averages (Fri May 31 2019 - 07:17:28 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 18:39:12 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 18:29:13 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 18:15:29 PDT)
- Re: [AMBER] graph (Thu May 30 2019 - 08:08:20 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 08:03:21 PDT)
- Re: [AMBER] PCA with a really giant trajectory (Tue May 28 2019 - 11:41:52 PDT)
- Re: [AMBER] hbond lifetime filesize issues (Tue May 21 2019 - 09:50:58 PDT)
- Re: [AMBER] DRMSD utility in cpptraj (Mon May 20 2019 - 12:33:46 PDT)
- Re: [AMBER] NetCDF trajectory file does not contain information about time/timestep (Mon May 20 2019 - 11:08:54 PDT)
- Re: [AMBER] Velocity rescaling between different temperatures? (Mon May 20 2019 - 09:33:25 PDT)
- Re: [AMBER] Velocity rescaling between different temperatures? (Mon May 20 2019 - 05:28:04 PDT)
- Re: [AMBER] NetCDF trajectory file does not contain information about time/timestep (Fri May 17 2019 - 07:25:00 PDT)
- Re: [AMBER] RMSF of combined trajectory (Fri May 17 2019 - 05:23:23 PDT)
- Re: [AMBER] Random segfaults (invalid memory reference) in sander (Wed May 15 2019 - 08:52:10 PDT)
- Re: [AMBER] hbond lifetime filesize issues (Wed May 15 2019 - 06:36:27 PDT)
- Re: [AMBER] Any help on how to implement it in cpptraj? (Thu May 09 2019 - 11:54:48 PDT)
- Re: [AMBER] SPAM bulk solvent free energy parameters (Thu May 09 2019 - 11:39:26 PDT)
- Re: [AMBER] Thermostat question (Thu May 09 2019 - 11:21:10 PDT)
- Re: [AMBER] Thermostat question (Wed May 08 2019 - 05:55:08 PDT)
- Re: [AMBER] CPPTRAJ OPENMP - MPI (Wed May 08 2019 - 04:23:21 PDT)
- Re: [AMBER] Distance calculation and distance matrix giving discrepant results (Fri May 03 2019 - 09:14:29 PDT)
- Re: [AMBER] Random segfaults (invalid memory reference) in sander (Fri May 03 2019 - 05:29:15 PDT)
- Re: [AMBER] Random segfaults (invalid memory reference) in sander (Fri May 03 2019 - 05:27:15 PDT)
- Re: [AMBER] CPPTRAJ gnu extension not working (Thu May 02 2019 - 05:34:12 PDT)
- Re: [AMBER] CPPTRAJ average residue-wise contact map (Thu May 02 2019 - 05:25:25 PDT)
David A Case
- Re: [AMBER] Question about sander running parallel (Fri May 31 2019 - 10:31:08 PDT)
- Re: [AMBER] make test fail (Fri May 31 2019 - 10:21:31 PDT)
- Re: [AMBER] Using a box of organic solvent (Fri May 31 2019 - 05:14:51 PDT)
- Re: [AMBER] anybody has any idea? (Thu May 30 2019 - 04:04:26 PDT)
- Re: [AMBER] Help compiling AMBER18 GPU Code- Cannot find compiler cl.exe in PATH (Thu May 30 2019 - 03:58:58 PDT)
- Re: [AMBER] error with loading HEM parameters for constph redox calcuations (Wed May 29 2019 - 09:03:23 PDT)
- Re: [AMBER] problem of srun (Wed May 29 2019 - 06:45:22 PDT)
- Re: [AMBER] amber 16 installation on Ubuntu 18 (Wed May 29 2019 - 04:58:12 PDT)
- Re: [AMBER] Changes to AmberTools antechamber Makefile (Wed May 29 2019 - 04:57:05 PDT)
- Re: [AMBER] Some basic question (Tue May 28 2019 - 10:51:29 PDT)
- Re: [AMBER] Installation of AMBER 18 regarding (Tue May 28 2019 - 10:43:50 PDT)
- Re: [AMBER] reduce info.log (Tue May 28 2019 - 10:35:07 PDT)
- Re: [AMBER] Problem in simulating peptide with modified amino acid - vlimit exceeded (Tue May 28 2019 - 04:45:22 PDT)
- Re: [AMBER] compiling Amber Tools 19 (Tue May 28 2019 - 04:38:55 PDT)
- Re: [AMBER] amber inputs (Thu May 23 2019 - 07:59:33 PDT)
- Re: [AMBER] Temperature variation in QM/MM simulation with AMBER18/G09 (Thu May 23 2019 - 06:00:40 PDT)
- Re: [AMBER] Regarding building of parallel version of AMBER18 in centos 7 (Wed May 22 2019 - 05:03:30 PDT)
- Re: [AMBER] Suggestion about proper ANTECHAMBER usage (Fri May 17 2019 - 06:25:17 PDT)
- Re: [AMBER] Bubbles during NPT and NVT simulations (Thu May 16 2019 - 05:05:25 PDT)
- Re: [AMBER] Crashed dynamics : connectivity (Wed May 15 2019 - 07:50:27 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't (Wed May 15 2019 - 06:08:40 PDT)
- Re: [AMBER] 3D-RISM options (Wed May 15 2019 - 05:46:55 PDT)
- Re: [AMBER] Solute free non-water solvent (Tue May 14 2019 - 10:34:58 PDT)
- Re: [AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide (Tue May 14 2019 - 06:12:31 PDT)
- Re: [AMBER] Average structure vs Individual frames (Tue May 14 2019 - 06:09:05 PDT)
- Re: [AMBER] amber18 parallel cpu make test hanging at first test (Tue May 14 2019 - 06:02:37 PDT)
- Re: [AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped) (Tue May 14 2019 - 05:55:43 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't (Mon May 13 2019 - 06:50:41 PDT)
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid (Mon May 13 2019 - 05:51:38 PDT)
- Re: [AMBER] MC barostat cause the system to stuck indefinitely (Mon May 13 2019 - 05:44:29 PDT)
- Re: [AMBER] continuous DNA (Thu May 09 2019 - 10:44:04 PDT)
- Re: [AMBER] NVidia backwards compatibility (Wed May 08 2019 - 05:14:42 PDT)
- Re: [AMBER] distance restraint failed in minimization and MD (Wed May 08 2019 - 05:09:24 PDT)
- Re: [AMBER] different energy values from mdout and cpptraj (Tue May 07 2019 - 06:01:20 PDT)
- Re: [AMBER] running qsub files in a single standalone workstation (Tue May 07 2019 - 04:16:58 PDT)
- Re: [AMBER] Random segfaults (invalid memory reference) in sander (Mon May 06 2019 - 07:52:18 PDT)
- Re: [AMBER] Ambertools2018/SQM installation (Mon May 06 2019 - 07:43:50 PDT)
- Re: [AMBER] Force field for nucleobases, nucleosides and nucleotides (Fri May 03 2019 - 06:40:36 PDT)
- Re: [AMBER] Simulation with Protein, cofactor and Ligand (Wed May 01 2019 - 10:53:53 PDT)
- Re: [AMBER] mol2 files for FEW (Wed May 01 2019 - 10:50:43 PDT)
- Re: [AMBER] Library for Phosphate ion (Wed May 01 2019 - 04:44:06 PDT)
David Case
- Re: [AMBER] parameter file for dUTP (Thu May 30 2019 - 18:43:37 PDT)
- Re: [AMBER] How to generate boron atom force field parameters (Thu May 30 2019 - 18:24:54 PDT)
- Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 (Thu May 30 2019 - 18:20:12 PDT)
- Re: [AMBER] rmsd (Mon May 27 2019 - 18:49:22 PDT)
- Re: [AMBER] compiling Amber Tools 19 (Mon May 27 2019 - 18:45:21 PDT)
- Re: [AMBER] Print Hessian matrix in (3,3) dimension (Mon May 27 2019 - 18:30:38 PDT)
- Re: [AMBER] Qm minimization, (Fri May 24 2019 - 04:42:33 PDT)
- Re: [AMBER] Force field for intrinsically disordered proteins (Sun May 19 2019 - 05:24:37 PDT)
- Re: [AMBER] check version (Sun May 05 2019 - 13:38:36 PDT)
- Re: [AMBER] AmberTools hardcodes library names into binaries (Sat May 04 2019 - 19:19:14 PDT)
David Cerutti
- Re: [AMBER] PCA with a really giant trajectory (Tue May 28 2019 - 11:47:56 PDT)
- Re: [AMBER] PCA with a really giant trajectory (Tue May 28 2019 - 10:49:15 PDT)
- [AMBER] PCA with a really giant trajectory (Sat May 25 2019 - 12:31:54 PDT)
- Re: [AMBER] nvidia tesla-t4 and amber (Wed May 15 2019 - 08:58:45 PDT)
- Re: [AMBER] AMBER 16 vs 18 on different cuda (Wed May 08 2019 - 13:17:12 PDT)
- Re: [AMBER] Thermostat question (Wed May 08 2019 - 00:22:16 PDT)
- Re: [AMBER] cuda test failing after installation (Tue May 07 2019 - 11:02:48 PDT)
- Re: [AMBER] [mjldehoon.yahoo.com: Files for Tutorial 32 (Deriving bonded parameters with mdgx)] (Fri May 03 2019 - 08:30:40 PDT)
Debarati DasGupta
- [AMBER] Volmap command in cpptraj followed by SPAM (Thu May 23 2019 - 06:59:28 PDT)
- Re: [AMBER] DRMSD utility in cpptraj (Tue May 21 2019 - 06:15:48 PDT)
- [AMBER] DRMSD utility in cpptraj (Fri May 17 2019 - 13:45:30 PDT)
- Re: [AMBER] Simulating Water Exchange to Buried Binding Sites (Fri May 17 2019 - 11:18:09 PDT)
- [AMBER] Simulating Water Exchange to Buried Binding Sites (Thu May 16 2019 - 06:21:44 PDT)
- Re: [AMBER] Energy shifted energy term (Fri May 10 2019 - 13:13:59 PDT)
- [AMBER] Energy shifted energy term (Thu May 09 2019 - 13:48:42 PDT)
- [AMBER] SPAM bulk solvent free energy parameters (Tue May 07 2019 - 06:36:51 PDT)
- Re: [AMBER] Any help on how to implement it in cpptraj? (Mon May 06 2019 - 13:27:46 PDT)
Dickson, Callum
- Re: [AMBER] tleap split lipid when it shouldn't (Mon May 13 2019 - 08:57:36 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't (Mon May 13 2019 - 07:49:49 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't (Mon May 13 2019 - 06:56:21 PDT)
Elena Gomez
- [AMBER] Selecting number of waters in tleap (Fri May 17 2019 - 01:09:35 PDT)
Elisa Pieri
- Re: [AMBER] Force field for nucleobases, nucleosides and nucleotides (Thu May 02 2019 - 15:31:19 PDT)
- [AMBER] Force field for nucleobases, nucleosides and nucleotides (Thu May 02 2019 - 14:10:06 PDT)
emanuele falbo
- [AMBER] Crashed dynamics : connectivity (Wed May 15 2019 - 05:59:49 PDT)
Erdem Yeler
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] (Sun May 05 2019 - 04:30:44 PDT)
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] (Sun May 05 2019 - 03:03:59 PDT)
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] (Sat May 04 2019 - 02:57:44 PDT)
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] (Sat May 04 2019 - 02:56:05 PDT)
- [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] (Fri May 03 2019 - 02:36:48 PDT)
- Re: [AMBER] Novel Force Field Parameters for Aromatic Dihedrals (Fri May 03 2019 - 02:25:00 PDT)
Fabian Glaser
- Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 (Wed May 29 2019 - 12:15:15 PDT)
- Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 (Wed May 29 2019 - 10:54:14 PDT)
- [AMBER] phosphor tyrosine bound to C5' terminal DA5 (Wed May 29 2019 - 07:04:19 PDT)
Feng Pan
- Re: [AMBER] umbrella sampling using pmemd in amber/2016 (Tue May 07 2019 - 09:26:58 PDT)
- Re: [AMBER] SMD using contact number (Thu May 02 2019 - 08:50:29 PDT)
Feng, Zimin
- Re: [AMBER] Are R.E.D. tools still a thing? (Fri May 03 2019 - 10:52:09 PDT)
- Re: [AMBER] FLAG_POINTERS in prmtop file (Fri May 03 2019 - 09:11:09 PDT)
- [AMBER] FLAG_POINTERS in prmtop file (Fri May 03 2019 - 08:10:33 PDT)
Gargi Borgohain
- Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file (Fri May 17 2019 - 02:45:31 PDT)
- [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file (Thu May 16 2019 - 02:38:29 PDT)
Gustaf Olsson
- Re: [AMBER] Ambertools2018/SQM installation (Mon May 06 2019 - 03:36:28 PDT)
Hai Nguyen
- Re: [AMBER] compiling Amber Tools 19 (Thu May 30 2019 - 11:22:52 PDT)
Hashemi, Mohtadin
- Re: [AMBER] compiling Amber Tools 19 (Thu May 30 2019 - 12:12:16 PDT)
- Re: [AMBER] compiling Amber Tools 19 (Thu May 30 2019 - 06:59:59 PDT)
Hirdesh Kumar
- [AMBER] rmsd (Mon May 27 2019 - 11:35:16 PDT)
Jaimes, Luis
- [AMBER] Error using mm_pbsa.pl binding energy calculations (Wed May 01 2019 - 17:44:23 PDT)
James Kress
- Re: [AMBER] NVidia backwards compatibility (Wed May 08 2019 - 06:43:11 PDT)
- [AMBER] NVidia backwards compatibility (Tue May 07 2019 - 12:43:34 PDT)
- Re: [AMBER] Random segfaults (invalid memory reference) in sander (Thu May 02 2019 - 10:28:48 PDT)
Jan Brezovsky
- [AMBER] Open position for doctoral candidate in biomolecular simulations (Fri May 17 2019 - 02:17:10 PDT)
Jason Swails
- Re: [AMBER] FLAG_POINTERS in prmtop file (Fri May 10 2019 - 12:25:48 PDT)
- Re: [AMBER] Are R.E.D. tools still a thing? (Fri May 10 2019 - 12:23:47 PDT)
- Re: [AMBER] Energy shifted energy term (Fri May 10 2019 - 12:04:04 PDT)
Jay Spencer
- [AMBER] Help compiling AMBER18 GPU Code- Cannot find compiler cl.exe in PATH (Wed May 29 2019 - 19:01:53 PDT)
Joan Torras
- Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file (Fri May 17 2019 - 03:47:00 PDT)
Jocelyn Sunseri
- [AMBER] Changes to AmberTools antechamber Makefile (Tue May 28 2019 - 10:58:47 PDT)
Jonathan Huihui
- Re: [AMBER] Distance calculation and distance matrix giving discrepant results (Fri May 03 2019 - 10:01:27 PDT)
- [AMBER] Distance calculation and distance matrix giving discrepant results (Thu May 02 2019 - 09:25:55 PDT)
Karl Kirschner
- Re: [AMBER] matching energies betwen amber-md and gromacs using amber parameters in both (Tue May 07 2019 - 00:21:37 PDT)
- Re: [AMBER] matching energies betwen amber-md and gromacs using amber parameters in both (Mon May 06 2019 - 03:32:28 PDT)
Kellon Belfon
- Re: [AMBER] Selecting number of waters in tleap (Fri May 17 2019 - 11:07:00 PDT)
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] (Fri May 03 2019 - 08:49:00 PDT)
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] (Fri May 03 2019 - 08:22:22 PDT)
Kenneth Huang
- Re: [AMBER] rmsd (Mon May 27 2019 - 18:18:27 PDT)
- Re: [AMBER] Velocity rescaling between different temperatures? (Mon May 20 2019 - 09:25:38 PDT)
- [AMBER] Velocity rescaling between different temperatures? (Fri May 17 2019 - 12:18:15 PDT)
Lorenzo Gontrani
- [AMBER] CPPTRAJ OPENMP - MPI (Wed May 08 2019 - 02:51:34 PDT)
Luca Codutti
- Re: [AMBER] nvidia tesla-t4 and amber (Wed May 15 2019 - 09:28:01 PDT)
- [AMBER] nvidia tesla-t4 and amber (Wed May 15 2019 - 08:46:36 PDT)
- [AMBER] Are R.E.D. tools still a thing? (Fri May 03 2019 - 10:17:35 PDT)
Marcos Serrou do Amaral
- Re: [AMBER] empty cein file redox potential calculations (Thu May 30 2019 - 05:38:51 PDT)
- Re: [AMBER] empty cein file redox potential calculations (Thu May 30 2019 - 05:03:43 PDT)
Margarita I. Bernal-Uruchurtu
- [AMBER] Random segfaults (invalid memory reference) in sander (Fri May 03 2019 - 02:11:59 PDT)
Markowska
- Re: [AMBER] NetCDF trajectory file does not contain information about time/timestep (Sat May 18 2019 - 12:46:30 PDT)
- [AMBER] Force field for intrinsically disordered proteins (Sat May 18 2019 - 05:11:46 PDT)
- [AMBER] NetCDF trajectory file does not contain information about time/timestep (Wed May 15 2019 - 11:12:57 PDT)
- Re: [AMBER] Thermostat question (Wed May 08 2019 - 13:32:46 PDT)
- [AMBER] Thermostat question (Tue May 07 2019 - 23:51:52 PDT)
maryam azimzadehirani
- [AMBER] jobs getting cancelled on cuda7 gpus (Fri May 24 2019 - 22:59:14 PDT)
Matias Machado
- Re: [AMBER] Lennard Jones parameters in frcmod (Thu May 23 2019 - 08:21:56 PDT)
- Re: [AMBER] Simulating Water Exchange to Buried Binding Sites (Fri May 17 2019 - 11:22:10 PDT)
- Re: [AMBER] Selecting number of waters in tleap (Fri May 17 2019 - 07:19:02 PDT)
- Re: [AMBER] Simulating Water Exchange to Buried Binding Sites (Fri May 17 2019 - 07:14:06 PDT)
- [AMBER] Releasing SIRAH lipids! A complete coarse-grained force field running on AMBER (Wed May 15 2019 - 11:30:57 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't (Wed May 15 2019 - 10:15:32 PDT)
- [AMBER] SIRAH force field goes quantum in AMBER (Fri May 03 2019 - 13:12:34 PDT)
Maximilien BERNE
- Re: [AMBER] tleap split lipid when it shouldn't (Mon May 20 2019 - 07:48:12 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't (Wed May 15 2019 - 07:17:52 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't (Wed May 15 2019 - 03:18:29 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't (Mon May 13 2019 - 08:23:28 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't (Mon May 13 2019 - 07:37:09 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't (Mon May 13 2019 - 07:32:03 PDT)
- [AMBER] tleap split lipid when it shouldn't (Mon May 13 2019 - 05:41:42 PDT)
Meng Wu
- [AMBER] How to generate boron atom force field parameters (Thu May 30 2019 - 03:53:24 PDT)
Michiel de Hoon
- [AMBER] Files for Tutorial 32 (Deriving bonded parameters with mdgx) (Fri May 03 2019 - 02:26:58 PDT)
Ming Tang
- [AMBER] amber 16 installation on Ubuntu 18 (Tue May 28 2019 - 21:45:12 PDT)
Nadine Homeyer
- Re: [AMBER] mol2 files for FEW (Mon May 20 2019 - 11:10:56 PDT)
- Re: [AMBER] running qsub files in a single standalone workstation (Tue May 07 2019 - 23:09:28 PDT)
Pacheco, Sayuri
- Re: [AMBER] Question regarding compatibility of Temperature replica exchange MD (TREMD) with constant pH MD (Fri May 03 2019 - 13:02:06 PDT)
- [AMBER] Question regarding compatibility of Temperature replica exchange MD (TREMD) with constant pH MD (Fri May 03 2019 - 11:48:35 PDT)
Pengfei Li
- Re: [AMBER] Error in step 3 of MCPB.py (Tue May 21 2019 - 08:50:36 PDT)
Pietro Aronica
- Re: [AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide (Tue May 14 2019 - 02:19:31 PDT)
- Re: [AMBER] three letter code for unprotonated carboxyglutamates (Tue May 07 2019 - 02:52:12 PDT)
Piotr Fajer
- [AMBER] Unequal distribution of water (Tue May 07 2019 - 14:26:29 PDT)
Pratul Agarwal
- Re: [AMBER] Catalysis mechanism of ATPase (Mon May 20 2019 - 15:59:27 PDT)
- Re: [AMBER] Missing file amber tutorial (Wed May 15 2019 - 11:32:55 PDT)
- Re: [AMBER] Missing file amber tutorial (Wed May 15 2019 - 11:12:02 PDT)
- Re: [AMBER] Entropy calculation for a protein homodimerization (Wed May 15 2019 - 04:47:16 PDT)
- Re: [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 (Tue May 14 2019 - 06:31:01 PDT)
- Re: [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 (Mon May 13 2019 - 07:24:10 PDT)
- Re: [AMBER] GPU versions: pmemd.cuda* (Thu May 09 2019 - 08:17:08 PDT)
- Re: [AMBER] pmemd.cuda "cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered" (Wed May 08 2019 - 09:09:44 PDT)
- Re: [AMBER] check version (Sun May 05 2019 - 07:51:40 PDT)
Pär Håkansson
- Re: [AMBER] Boron QM/MM (Fri May 31 2019 - 05:55:05 PDT)
- [AMBER] Boron QM/MM (Fri May 31 2019 - 04:08:00 PDT)
Qinghua Liao
- [AMBER] continuous DNA (Thu May 09 2019 - 06:39:00 PDT)
Rajarshi Roy
- Re: [AMBER] Regarding building of parallel version of AMBER18 in centos 7 (Thu May 23 2019 - 06:40:42 PDT)
- [AMBER] Regarding building of parallel version of AMBER18 in centos 7 (Tue May 21 2019 - 20:49:41 PDT)
- Re: [AMBER] Regarding GTX 1050 Ti (Sat May 11 2019 - 11:51:28 PDT)
- [AMBER] Regarding GTX 1050 Ti (Fri May 10 2019 - 20:22:09 PDT)
Rakesh Srivastava
- Re: [AMBER] Entropy calculation for a protein homodimerization (Wed May 15 2019 - 05:20:31 PDT)
- [AMBER] Entropy calculation for a protein homodimerization (Wed May 15 2019 - 01:47:53 PDT)
Ravi Abrol
- Re: [AMBER] amber18 parallel cpu make test hanging at first test (Tue May 14 2019 - 17:55:22 PDT)
- Re: [AMBER] cuda test failing after installation (Mon May 13 2019 - 11:52:43 PDT)
- [AMBER] amber18 parallel cpu make test hanging at first test (Mon May 13 2019 - 11:47:18 PDT)
- Re: [AMBER] cuda test failing after installation (Tue May 07 2019 - 12:43:28 PDT)
- Re: [AMBER] cuda test failing after installation (Tue May 07 2019 - 10:26:54 PDT)
razie yousefi
- [AMBER] Solute free non-water solvent (Tue May 14 2019 - 08:01:17 PDT)
Reber, David
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 20:55:32 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 20:03:49 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 19:33:47 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 19:17:53 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 18:46:20 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 18:33:31 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 18:23:39 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 17:31:45 PDT)
- [AMBER] Radgyr or distance averages (Wed May 29 2019 - 20:24:20 PDT)
- Re: [AMBER] hbond lifetime filesize issues (Tue May 21 2019 - 19:09:20 PDT)
- Re: [AMBER] hbond lifetime filesize issues (Wed May 15 2019 - 22:02:36 PDT)
- Re: [AMBER] hbond lifetime filesize issues (Wed May 15 2019 - 18:52:17 PDT)
- [AMBER] hbond lifetime filesize issues (Wed May 15 2019 - 02:53:13 PDT)
- [AMBER] Center of mass velocity autocorrelation function (Sun May 12 2019 - 18:29:33 PDT)
- [AMBER] Residence time around ions (Sun May 12 2019 - 03:58:43 PDT)
Rinsha Chk
- Re: [AMBER] RMSF of combined trajectory (Sun May 19 2019 - 21:23:40 PDT)
- Re: [AMBER] RMSF of combined trajectory (Fri May 17 2019 - 00:08:53 PDT)
- Re: [AMBER] RMSF of combined trajectory (Thu May 16 2019 - 22:26:58 PDT)
- [AMBER] RMSF of combined trajectory (Thu May 16 2019 - 04:43:37 PDT)
Ross Walker
- Re: [AMBER] Regarding GTX 1050 Ti (Sat May 11 2019 - 11:23:40 PDT)
Ruth Helena Tichauer
- [AMBER] set RA, RT and n_partition in adQM/MM run (Wed May 15 2019 - 03:57:38 PDT)
- Re: [AMBER] Guidance on WHAM (Fri May 03 2019 - 08:18:48 PDT)
- Re: [AMBER] Guidance on WHAM (Fri May 03 2019 - 08:09:38 PDT)
Ryan Pavlovicz
- Re: [AMBER] 3D-RISM options (Wed May 15 2019 - 07:45:41 PDT)
- Re: [AMBER] 3D-RISM options (Tue May 14 2019 - 23:01:18 PDT)
- Re: [AMBER] 3D-RISM options (Tue May 14 2019 - 17:10:31 PDT)
- [AMBER] 3D-RISM options (Tue May 14 2019 - 14:45:27 PDT)
Sadaf Rani
- [AMBER] Question about sander running parallel (Fri May 31 2019 - 09:39:23 PDT)
- [AMBER] make test fail (Fri May 31 2019 - 09:24:55 PDT)
- [AMBER] Minimization input (Wed May 29 2019 - 03:29:46 PDT)
- Re: [AMBER] reduce info.log (Wed May 29 2019 - 03:08:02 PDT)
- [AMBER] reduce info.log (Tue May 28 2019 - 04:38:07 PDT)
- Re: [AMBER] Missing file amber tutorial (Tue May 28 2019 - 02:01:02 PDT)
- [AMBER] Missing file amber tutorial (Wed May 15 2019 - 11:06:10 PDT)
- Re: [AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped) (Wed May 15 2019 - 11:00:28 PDT)
- [AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped) (Mon May 13 2019 - 08:56:06 PDT)
- [AMBER] Failed to generate parameters (Sat May 11 2019 - 08:48:41 PDT)
- [AMBER] Fwd: The unperturbed charge of the unit: 4.003000 is not zero (Sat May 11 2019 - 04:16:07 PDT)
Saikat Dutta chowdhury
- [AMBER] Problem in simulating peptide with modified amino acid - vlimit exceeded (Tue May 28 2019 - 04:07:07 PDT)
- Re: [AMBER] Suggestion about proper ANTECHAMBER usage (Fri May 17 2019 - 06:54:27 PDT)
- [AMBER] Suggestion about proper ANTECHAMBER usage (Fri May 17 2019 - 04:38:52 PDT)
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid (Mon May 13 2019 - 21:23:06 PDT)
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid (Mon May 13 2019 - 03:41:15 PDT)
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid (Mon May 13 2019 - 00:46:40 PDT)
- [AMBER] Problem with preparing parameters with antechamber for modified amino acid (Sat May 11 2019 - 23:40:19 PDT)
Saikat Pal
- Re: [AMBER] Capping a dipeptide with Boc (Wed May 08 2019 - 09:44:32 PDT)
- Re: [AMBER] Capping a dipeptide with Boc (Wed May 08 2019 - 09:16:24 PDT)
- Re: [AMBER] Capping a dipeptide with Boc (Wed May 08 2019 - 05:15:12 PDT)
- [AMBER] Capping a dipeptide with Boc (Wed May 08 2019 - 04:04:50 PDT)
Sally Pias
- Re: [AMBER] tleap split lipid when it shouldn't (Wed May 15 2019 - 15:12:15 PDT)
SARAH JEANNE LEFAVE
- [AMBER] deselect residues for step1 model in MCPB.py (Wed May 29 2019 - 09:39:30 PDT)
scanya.interia.eu
- Re: [AMBER] Random segfaults (invalid memory reference) in sander (Fri May 03 2019 - 07:23:10 PDT)
Schröder, David Christopher
- Re: [AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide (Tue May 14 2019 - 07:20:27 PDT)
Shahila Muhammed
- Re: [AMBER] Error in step 3 of MCPB.py (Wed May 22 2019 - 05:20:42 PDT)
- [AMBER] Error in step 3 of MCPB.py (Fri May 17 2019 - 01:02:55 PDT)
Shenglong Wang
- Re: [AMBER] nvidia tesla-t4 and amber (Wed May 15 2019 - 08:52:12 PDT)
Shilpa Gupta
- [AMBER] Optimization of geometry in xleap (Wed May 29 2019 - 23:21:05 PDT)
Sina
- [AMBER] Some basic question (Fri May 24 2019 - 09:18:41 PDT)
- [AMBER] Qm minimization, (Fri May 24 2019 - 03:22:47 PDT)
- [AMBER] amber inputs (Thu May 23 2019 - 06:44:31 PDT)
- Re: [AMBER] Ambertools2018/SQM installation (Mon May 06 2019 - 09:24:44 PDT)
- [AMBER] Ambertools2018/SQM installation (Mon May 06 2019 - 01:59:31 PDT)
Sowmya Indrakumar
- Re: [AMBER] Library for Phosphate ion (Wed May 01 2019 - 06:19:14 PDT)
Stefan.Guessregen.sanofi.com
- [AMBER] GCC 2019, November 3-5 in Mainz, Deadline extendend to June 23, 2019 (Mon May 27 2019 - 23:20:14 PDT)
Stefano Motta
- [AMBER] Lennard Jones parameters in frcmod (Thu May 23 2019 - 07:31:17 PDT)
- [AMBER] Bubbles during NPT and NVT simulations (Thu May 16 2019 - 02:56:24 PDT)
Stephan Schott
- Re: [AMBER] Protein-Lipid Bilayer PDB preparation Issue(s) (Mon May 27 2019 - 11:49:56 PDT)
- Re: [AMBER] Protein-Lipid Bilayer PDB preparation Issue(s) (Mon May 27 2019 - 10:17:42 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't (Wed May 15 2019 - 10:42:50 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't (Wed May 15 2019 - 10:35:22 PDT)
sunyeping
- Re: [AMBER] parameter file for dUTP (Thu May 30 2019 - 14:38:11 PDT)
- [AMBER] parameter file for dUTP (Thu May 30 2019 - 06:03:54 PDT)
- [AMBER] Catalysis mechanism of ATPase (Sun May 19 2019 - 04:29:35 PDT)
Tanusree S
- [AMBER] three letter code for unprotonated carboxyglutamates (Tue May 07 2019 - 02:45:25 PDT)
Thomas C. Bishop
- Re: [AMBER] continuous DNA (Thu May 09 2019 - 12:33:40 PDT)
Thomas Cheatham
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 20:07:06 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 19:43:02 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 19:23:11 PDT)
- Re: [AMBER] Radgyr or distance averages (Thu May 30 2019 - 19:07:01 PDT)
Thomas Gaillard
- [AMBER] MMPBSA radiopt effect on EDISPER (Mon May 13 2019 - 09:40:57 PDT)
Tyler Luchko (Lists)
- Re: [AMBER] 3D-RISM options (Wed May 15 2019 - 10:17:12 PDT)
- Re: [AMBER] 3D-RISM options (Tue May 14 2019 - 17:17:38 PDT)
- Re: [AMBER] 3D-RISM options (Tue May 14 2019 - 15:44:24 PDT)
Vaibhav Dixit
- Re: [AMBER] error with loading HEM parameters for constph redox calcuations (Fri May 31 2019 - 12:32:03 PDT)
- Re: [AMBER] error with loading HEM parameters for constph redox calcuations (Fri May 31 2019 - 12:05:26 PDT)
- Re: [AMBER] empty cein file redox potential calculations (Thu May 30 2019 - 07:38:16 PDT)
- Re: [AMBER] empty cein file redox potential calculations (Thu May 30 2019 - 05:16:45 PDT)
- [AMBER] empty cein file redox potential calculations (Thu May 30 2019 - 04:36:37 PDT)
- Re: [AMBER] error with loading HEM parameters for constph redox calcuations (Thu May 30 2019 - 02:35:41 PDT)
- Re: [AMBER] error with loading HEM parameters for constph redox calcuations (Wed May 29 2019 - 13:52:32 PDT)
- [AMBER] error with loading HEM parameters for constph redox calcuations (Wed May 29 2019 - 07:53:28 PDT)
Veenis, Andrew Jay
- Re: [AMBER] issues with pmemd.cuda (Fri May 03 2019 - 12:20:43 PDT)
viktor drobot
- [AMBER] AmberTools hardcodes library names into binaries (Sat May 04 2019 - 03:57:57 PDT)
Vlad Cojocaru
- Re: [AMBER] compiling Amber Tools 19 (Tue May 28 2019 - 05:37:07 PDT)
- Re: [AMBER] compiling Amber Tools 19 (Tue May 28 2019 - 01:33:15 PDT)
- Re: [AMBER] compiling Amber Tools 19 (Mon May 27 2019 - 05:14:32 PDT)
- [AMBER] compiling Amber Tools 19 (Mon May 27 2019 - 04:42:38 PDT)
wujue
- [AMBER] distance restraint failed in minimization and MD (Tue May 07 2019 - 19:38:40 PDT)
Xiaoyu Wang
- [AMBER] AMBER 16 vs 18 on different cuda (Wed May 08 2019 - 13:08:11 PDT)
xmgign.126.com
- [AMBER] How to generate the correct force field parameter for a large molecule? (Sun May 26 2019 - 23:27:44 PDT)
Yin, Guowei
- Re: [AMBER] Average structure vs Individual frames (Mon May 13 2019 - 19:19:16 PDT)
- [AMBER] Average structure vs Individual frames (Mon May 13 2019 - 18:16:59 PDT)
- [AMBER] GPU versions: pmemd.cuda* (Thu May 09 2019 - 08:11:05 PDT)
Zachary Fallon
- Re: [AMBER] parameter file for dUTP (Thu May 30 2019 - 15:12:07 PDT)
- Re: [AMBER] parameter file for dUTP (Thu May 30 2019 - 10:55:20 PDT)
Zhiyi Wu
- [AMBER] MC barostat cause the system to stuck indefinitely (Sat May 11 2019 - 14:10:13 PDT)
杨明俊
- Re: [AMBER] Different potential energies between recomputed and original simulations from PMEMD? (Fri May 24 2019 - 05:02:28 PDT)
- [AMBER] Different potential energies between recomputed and original simulations from PMEMD? (Fri May 24 2019 - 03:14:32 PDT)

Amber Archive May 2019 by author