Amber Archive Nov 2012: by author

. mirage
- [AMBER] workstation (Mon Nov 05 2012 - 08:45:39 PST)
adarm.nencki.gov.pl
- Re: [AMBER] ptraj clustering problem (segmentation fault) (Mon Nov 26 2012 - 13:21:33 PST)
- [AMBER] ptraj clustering problem (segmentation fault) (Mon Nov 26 2012 - 05:25:20 PST)
Adelene Sim
- [AMBER] MMPBSA.py "timer: need to reset the time before start" (Sun Nov 04 2012 - 18:51:49 PST)
Alan
- Re: [AMBER] Antechamber and GTP (Thu Nov 15 2012 - 03:47:02 PST)
- [AMBER] Will Ptraj image the coordinates after rms fitting? (Tue Nov 06 2012 - 23:12:13 PST)
Albert
- [AMBER] R.E.D calculation cannot be used for CHARMM FF? (Wed Nov 28 2012 - 00:57:19 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 07:02:17 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 06:36:33 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 05:56:39 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 05:39:51 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 05:37:52 PST)
- [AMBER] is AMBER FF good enough for long time scaled MD? (Tue Nov 20 2012 - 23:17:54 PST)
- Re: [AMBER] Odp: Re: problem for lipid GAFF (Wed Nov 14 2012 - 01:57:44 PST)
- Re: [AMBER] problem for lipid GAFF (Tue Nov 13 2012 - 23:41:30 PST)
- Re: [AMBER] problem for lipid GAFF (Tue Nov 13 2012 - 09:12:38 PST)
- [AMBER] problem for lipid GAFF (Tue Nov 13 2012 - 02:18:13 PST)
Alex Rodriguez
- Re: [AMBER] strange deprotonation in QM/MM (Thu Nov 22 2012 - 02:34:09 PST)
Andreas Goetz
- [AMBER] QM/MM bugfix for semiempirical NDDO code available, soon (Fri Nov 16 2012 - 17:16:04 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 (Thu Nov 15 2012 - 15:33:50 PST)
- Re: [AMBER] AMBER-ORCA (Thu Nov 15 2012 - 13:38:42 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 (Wed Nov 14 2012 - 13:06:40 PST)
- Re: [AMBER] AMBER-Gaussian and Infrared (Sat Nov 03 2012 - 14:33:45 PDT)
Anogna
- [AMBER] Error in script file while running mm_pbsa.pl (Wed Nov 14 2012 - 23:32:20 PST)
anyiphysics.gmail.com
- Re: [AMBER] antechamber limitation on molecule size (Thu Nov 08 2012 - 08:44:36 PST)
- Re: [AMBER] antechamber limitation on molecule size (Wed Nov 07 2012 - 18:21:21 PST)
- Re: [AMBER] about angle restraint (Tue Nov 06 2012 - 16:48:04 PST)
- Re: [AMBER] about angle restraint (Tue Nov 06 2012 - 13:11:40 PST)
- [AMBER] about angle restraint (Tue Nov 06 2012 - 11:53:22 PST)
- Re: [AMBER] antechamber limitation on molecule size (Wed Oct 31 2012 - 18:27:50 PDT)
Aron Broom
- Re: [AMBER] MM PBSA error calculating entropy (Tue Nov 13 2012 - 15:36:54 PST)
- [AMBER] MM PBSA error calculating entropy (Tue Nov 13 2012 - 13:52:03 PST)
- Re: [AMBER] Primary structur to 3D structure (Thu Nov 08 2012 - 14:05:30 PST)
- Re: [AMBER] different force fields for different molecules in leap (Thu Nov 08 2012 - 08:10:31 PST)
- Re: [AMBER] Multi-protein simulation in a box (Thu Nov 08 2012 - 08:04:43 PST)
- Re: [AMBER] antechamber limitation on molecule size (Wed Nov 07 2012 - 18:34:20 PST)
- Re: [AMBER] NAMD failed to read Amber parm file (Wed Nov 07 2012 - 08:05:37 PST)
- Re: [AMBER] Energy Analysis from Trajectory (Tue Nov 06 2012 - 22:24:28 PST)
- [AMBER] Energy Analysis from Trajectory (Tue Nov 06 2012 - 22:07:25 PST)
- Re: [AMBER] tleap not recognizing Na+ (Mon Nov 05 2012 - 10:58:37 PST)
- Re: [AMBER] Clarifications in umbrella sampling (Mon Nov 05 2012 - 08:45:45 PST)
- Re: [AMBER] Clarifications in umbrella sampling (Sun Nov 04 2012 - 22:00:37 PST)
Aust, Susanne
- [AMBER] unsubscribe (Tue Nov 20 2012 - 01:13:01 PST)
baogen duan
- [AMBER] large value of "fglen" and "cglen"of iAPBS initiation during MMPBSA python script calculation (Thu Nov 15 2012 - 17:31:18 PST)
- [AMBER] No radius found for Mg+ using mm_pbsa.pl script (Fri Nov 09 2012 - 01:18:25 PST)
- Re: [AMBER] error of MMPBSA calculation using the prmtop and inpcrd generated by Chamber program (Wed Nov 07 2012 - 01:12:36 PST)
- [AMBER] error of MMPBSA calculation using the prmtop and inpcrd generated by Chamber program (Tue Nov 06 2012 - 18:25:19 PST)
- [AMBER] solvation free enrgy calculation using PB equation. (Thu Nov 01 2012 - 01:56:51 PDT)
- Re: [AMBER] error when Chamber dealing with DNA, RNA and ATP (Wed Oct 31 2012 - 19:40:53 PDT)
Baptiste Legrand
- [AMBER] Theorical ramachandran map/energy map of modified residues (Fri Nov 16 2012 - 09:25:13 PST)
- Re: [AMBER] "vlimit exceeded for step ..." during SA protocol (Tue Nov 13 2012 - 07:44:59 PST)
- Re: [AMBER] "vlimit exceeded for step ..." during SA protocol (Thu Nov 08 2012 - 01:28:27 PST)
- [AMBER] "vlimit exceeded for step ..." during SA protocol (Wed Nov 07 2012 - 01:25:59 PST)
Ben Roberts
- [AMBER] Amber 12 and PGI compilers >= 12.5 (Wed Nov 28 2012 - 15:09:23 PST)
BERGY
- Re: [AMBER] best tutorials (Tue Nov 06 2012 - 20:26:33 PST)
- Re: [AMBER] deprotonated serine (Fri Nov 02 2012 - 10:19:27 PDT)
- Re: [AMBER] Amber12 Parrell Installation Error (Fri Nov 02 2012 - 10:15:10 PDT)
- [AMBER] Amber12 PETASCALE Benchmarking. (Thu Nov 01 2012 - 22:09:02 PDT)
Bill Miller III
- Re: [AMBER] definition of receptor_mask and ligand_mask using MMPBSA method (Mon Nov 26 2012 - 04:39:31 PST)
- Re: [AMBER] error of MMPBSA calculation using the prmtop and inpcrd generated by Chamber program (Tue Nov 06 2012 - 18:29:49 PST)
- Re: [AMBER] references ? (Thu Nov 01 2012 - 12:33:24 PDT)
Bill Ross
- Re: [AMBER] error in heating process (Tue Nov 27 2012 - 23:07:25 PST)
- Re: [AMBER] Tleap crash while loading frcmod (Mon Nov 12 2012 - 21:41:36 PST)
- Re: [AMBER] Generating a solvent Box from organic solvent (Mon Nov 12 2012 - 17:55:46 PST)
bin wang
- Re: [AMBER] how to calculate binding energy of one receptor and two ligands? (Fri Nov 02 2012 - 10:30:22 PDT)
- [AMBER] how to calculate binding energy of one receptor and two ligands? (Fri Nov 02 2012 - 08:53:14 PDT)
Brent Krueger
- Re: [AMBER] AMBER-Gaussian and Infrared (Sun Nov 04 2012 - 03:37:30 PST)
Brian Radak
- Re: [AMBER] AMBER-ORCA-Freq (Fri Nov 16 2012 - 09:14:25 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 (Thu Nov 15 2012 - 09:30:47 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 (Wed Nov 14 2012 - 11:37:55 PST)
- Re: [AMBER] Multi-protein simulation in a box (Thu Nov 08 2012 - 08:50:16 PST)
- Re: [AMBER] AMBER-Gaussian and Infrared (Sat Nov 03 2012 - 10:05:33 PDT)
Brown, Kyle
- Re: [AMBER] Image problems with IWRAP=1 (Tue Nov 06 2012 - 14:52:03 PST)
- [AMBER] Image problems with IWRAP=1 (Tue Nov 06 2012 - 11:57:05 PST)
Brown, Paul
- Re: [AMBER] compiler errors (Fri Nov 09 2012 - 04:07:58 PST)
- Re: [AMBER] compiler errors (Thu Nov 08 2012 - 04:32:20 PST)
- [AMBER] compiler errors (Tue Nov 06 2012 - 08:06:04 PST)
Carlos Simmerling
- Re: [AMBER] calculation of protein-DNA complex structure (Tue Nov 27 2012 - 08:43:37 PST)
- Re: [AMBER] Theorical ramachandran map/energy map of modified residues (Fri Nov 16 2012 - 09:45:50 PST)
Cecilia Lindgren
- [AMBER] Parameters for amide bond isosteres (Thu Nov 08 2012 - 03:49:38 PST)
Changqing Yan
- [AMBER] force field file problem (Thu Nov 01 2012 - 06:16:08 PDT)
Christina Bergonzo
- Re: [AMBER] Forcefield (Wed Nov 21 2012 - 12:34:23 PST)
- Re: [AMBER] using nudged elastic band method with explicit solvent (Thu Nov 08 2012 - 08:35:07 PST)
- Re: [AMBER] implementation of string method to find minimum free energy paths in Amber (Thu Nov 01 2012 - 07:28:07 PDT)
colvin
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop -rdparm: a parameter array overflowed (Thu Nov 29 2012 - 16:15:35 PST)
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop -rdparm: a parameter array overflowed (Tue Nov 27 2012 - 21:46:11 PST)
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop (Tue Nov 27 2012 - 01:16:44 PST)
Daniel Roe
- Re: [AMBER] Reading DESMOND MD trajectory files in CPPTRAJ... (Tue Nov 27 2012 - 16:42:24 PST)
- Re: [AMBER] ptraj grid by center of mass (Mon Nov 26 2012 - 08:55:15 PST)
- Re: [AMBER] ptraj clustering problem (segmentation fault) (Mon Nov 26 2012 - 08:49:43 PST)
- Re: [AMBER] trajout command in ptraj (Mon Nov 19 2012 - 08:33:50 PST)
- Re: [AMBER] Problem with "make install" after "./configure intel" (Tue Nov 13 2012 - 13:25:59 PST)
- Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj (Tue Nov 13 2012 - 07:20:05 PST)
- Re: [AMBER] cppparmstrip command provokes segmentation fault (Tue Nov 13 2012 - 07:16:26 PST)
- Re: [AMBER] Dipole from a mask (Fri Nov 09 2012 - 07:05:09 PST)
- Re: [AMBER] Dipole from a mask (Thu Nov 08 2012 - 08:05:29 PST)
- Re: [AMBER] Image problems with IWRAP=1 (Wed Nov 07 2012 - 12:20:37 PST)
- Re: [AMBER] Image problems with IWRAP=1 (Tue Nov 06 2012 - 15:04:46 PST)
- Re: [AMBER] Image problems with IWRAP=1 (Tue Nov 06 2012 - 12:36:19 PST)
- Re: [AMBER] Dipole from a mask (Tue Nov 06 2012 - 12:31:42 PST)
Daniel Sindhikara
- Re: [AMBER] sander.MPI (Wed Nov 28 2012 - 23:56:34 PST)
- Re: [AMBER] Tleap crash while loading frcmod (Mon Nov 12 2012 - 22:00:12 PST)
- [AMBER] Tleap crash while loading frcmod (Mon Nov 12 2012 - 20:25:59 PST)
Daniel Álvarez García
- Re: [AMBER] ptraj grid by center of mass (Mon Nov 26 2012 - 10:03:08 PST)
- [AMBER] ptraj grid by center of mass (Mon Nov 26 2012 - 05:55:01 PST)
David A Case
- Re: [AMBER] sander.MPI (Wed Nov 28 2012 - 07:29:55 PST)
- Re: [AMBER] error in heating process (Wed Nov 28 2012 - 06:16:36 PST)
- Re: [AMBER] Antechamber-- Creating inputs for Ammonium-Borane (Tue Nov 27 2012 - 04:47:15 PST)
- Re: [AMBER] calculation of protein-DNA complex structure (Tue Nov 27 2012 - 04:44:54 PST)
- Re: [AMBER] [PATCH 1/8] AmberTools: Fix buffer overflows in mdgx, nab and ptraj (Mon Nov 26 2012 - 05:31:36 PST)
- Re: [AMBER] Problem of atom typing for the LYN residue? (Mon Nov 26 2012 - 05:18:26 PST)
- Re: [AMBER] Heating process- amber 8 regarding (Mon Nov 26 2012 - 05:10:12 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 04:37:00 PST)
- Re: [AMBER] Amber radii of ions (Mon Nov 19 2012 - 04:57:21 PST)
- Re: [AMBER] Can I mix Glycam and Gaff in a small molecule? (Mon Nov 19 2012 - 04:56:25 PST)
- Re: [AMBER] Antechamber and GTP (Thu Nov 15 2012 - 05:06:59 PST)
- Re: [AMBER] AMBER/ORCA (Thu Nov 15 2012 - 05:02:32 PST)
- Re: [AMBER] Energy Analysis from Trajectory (Thu Nov 15 2012 - 04:57:51 PST)
- Re: [AMBER] Antechamber and GTP (Wed Nov 14 2012 - 09:30:27 PST)
- Re: [AMBER] Regarding RNA Duplex formation (Wed Nov 14 2012 - 09:26:37 PST)
- Re: [AMBER] NOE calculation (Tue Nov 13 2012 - 05:18:07 PST)
- Re: [AMBER] Amber Error : Segmentation fault (Tue Nov 13 2012 - 05:10:20 PST)
- Re: [AMBER] Tleap crash while loading frcmod (Tue Nov 13 2012 - 05:07:32 PST)
- Re: [AMBER] Regarding Quadruplex Formation (Fri Nov 09 2012 - 17:53:04 PST)
- Re: [AMBER] Heme iron definition: Atom type missing (Fri Nov 09 2012 - 17:44:03 PST)
- Re: [AMBER] Obtain trajectory coordinates from LMOD minimization (Fri Nov 09 2012 - 05:01:39 PST)
- Re: [AMBER] bond missing in phosphate group after antechamber run (Thu Nov 08 2012 - 06:56:09 PST)
- Re: [AMBER] "vlimit exceeded for step ..." during SA protocol (Wed Nov 07 2012 - 06:46:22 PST)
- Re: [AMBER] questions about thermodynamic integration atom name and order (Wed Nov 07 2012 - 06:36:52 PST)
- Re: [AMBER] questions about thermodynamic integration atom name and order (Wed Nov 07 2012 - 06:36:44 PST)
- Re: [AMBER] Image problems with IWRAP=1 (Tue Nov 06 2012 - 12:16:44 PST)
- Re: [AMBER] about angle restraint (Tue Nov 06 2012 - 12:13:06 PST)
- Re: [AMBER] questions about thermodynamic integration atom name and order (Tue Nov 06 2012 - 12:06:20 PST)
- Re: [AMBER] tleap not recognizing Na+ (Mon Nov 05 2012 - 12:11:17 PST)
- Re: [AMBER] Cannot setting AMBERHOME on ubuntu 12.04 (Fri Nov 02 2012 - 06:30:37 PDT)
- Re: [AMBER] force field file problem (Thu Nov 01 2012 - 11:47:46 PDT)
- Re: [AMBER] solvation free enrgy calculation using PB equation. (Thu Nov 01 2012 - 10:37:42 PDT)
- Re: [AMBER] antechamber limitation on molecule size (Thu Nov 01 2012 - 10:34:59 PDT)
David Condon
- [AMBER] tleap not recognizing Na+ (Mon Nov 05 2012 - 10:23:40 PST)
dbaogen
- [AMBER] UTP and CTP amber force field parameters (Tue Nov 27 2012 - 04:43:54 PST)
- [AMBER] definition of receptor_mask and ligand_mask using MMPBSA method (Mon Nov 26 2012 - 04:30:09 PST)
- [AMBER] Magnesium ion (Mg2+) simulation (Tue Nov 20 2012 - 18:24:21 PST)
- [AMBER] very large value of "fglen" and "cglen" during MMPBSA.py calculatio using sander.APBS (Thu Nov 15 2012 - 05:13:13 PST)
Devlina Chakravarty
- [AMBER] Amber radii of ions (Sun Nov 18 2012 - 23:24:00 PST)
Dickson, Callum
- Re: [AMBER] problem for lipid GAFF (Tue Nov 13 2012 - 09:00:00 PST)
Dmitry Mukha
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE (Wed Nov 14 2012 - 10:21:09 PST)
- [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE (Wed Nov 14 2012 - 00:52:30 PST)
Eliana Asciutto
- [AMBER] Sorry for the previous email (Fri Nov 23 2012 - 07:33:03 PST)
- Re: [AMBER] Happy Thanksgiving!!!! (Fri Nov 23 2012 - 07:06:34 PST)
Elise Duboué-Dijon
- Re: [AMBER] Problem to run sander with more than 60 atom types (Tue Nov 27 2012 - 06:32:34 PST)
- Re: [AMBER] Problem to run sander with more than 60 atom types (Tue Nov 27 2012 - 03:20:48 PST)
- [AMBER] Problem to run sander with more than 60 atom types (Thu Nov 22 2012 - 00:40:12 PST)
Esam Tolba
- [AMBER] Cannot match namelist object name scee (Tue Nov 06 2012 - 06:26:47 PST)
Fabian Glaser
- Re: [AMBER] sander.MPI (Thu Nov 29 2012 - 05:54:06 PST)
- Re: [AMBER] sander.MPI (Thu Nov 29 2012 - 05:44:05 PST)
- Re: [AMBER] sander.MPI (Thu Nov 29 2012 - 05:18:23 PST)
- Re: [AMBER] sander.MPI (Wed Nov 28 2012 - 22:43:50 PST)
- [AMBER] sander.MPI (Wed Nov 28 2012 - 06:30:57 PST)
- [AMBER] best tutorials (Tue Nov 06 2012 - 06:32:26 PST)
- Re: [AMBER] no leaprc in search path (Mon Nov 05 2012 - 06:18:55 PST)
- Re: [AMBER] no leaprc in search path (Sun Nov 04 2012 - 07:24:16 PST)
- [AMBER] no leaprc in search path (Sun Nov 04 2012 - 06:37:14 PST)
Faez Iqbal khan
- [AMBER] Urgent (Sun Nov 11 2012 - 23:14:23 PST)
Fernando Martín García
- Re: [AMBER] GPU and ntpr (Fri Nov 30 2012 - 01:16:38 PST)
- Re: [AMBER] GPU and ntpr (Tue Nov 27 2012 - 03:46:02 PST)
- [AMBER] GPU and ntpr (Fri Nov 23 2012 - 03:14:41 PST)
- Re: [AMBER] Antechamber and GTP (Fri Nov 16 2012 - 08:21:15 PST)
- Re: [AMBER] Antechamber and GTP (Fri Nov 16 2012 - 04:09:59 PST)
- [AMBER] Antechamber and GTP (Wed Nov 14 2012 - 02:56:42 PST)
filip fratev
- [AMBER] Kepler II (K20) benchmark results? (Thu Nov 15 2012 - 08:59:25 PST)
fmgarcia.cbm.uam.es
- Re: [AMBER] Antechamber and GTP (Thu Nov 15 2012 - 00:31:52 PST)
francesco oteri
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 04:03:31 PST)
FyD
- Re: [AMBER] R.E.D calculation cannot be used for CHARMM FF? (Thu Nov 29 2012 - 13:27:21 PST)
- Re: [AMBER] Antechamber - Problem with protonated oxygen (Wed Nov 28 2012 - 01:02:57 PST)
- Re: [AMBER] Antechamber - Problem with protonated oxygen (Tue Nov 27 2012 - 22:05:58 PST)
- Re: [AMBER] Antechamber-- Creating inputs for Ammonium-Borane (Tue Nov 27 2012 - 21:48:46 PST)
- Re: [AMBER] UTP and CTP amber force field parameters (Tue Nov 27 2012 - 21:45:55 PST)
- Re: [AMBER] Antechamber and GTP (Fri Nov 16 2012 - 08:56:28 PST)
- [AMBER] Problem of atom typing for the LYN residue? (Wed Nov 14 2012 - 01:53:46 PST)
- Re: [AMBER] antechamber limitation on molecule size (Thu Nov 08 2012 - 01:55:44 PST)
- Re: [AMBER] How to use q4md-CD? (Wed Nov 07 2012 - 00:22:13 PST)
- Re: [AMBER] How to use q4md-CD? (Mon Nov 05 2012 - 13:29:56 PST)
- Re: [AMBER] [Private q4md] R.E.D. Server: Private assistance (Mon Nov 05 2012 - 12:15:33 PST)
- Re: [AMBER] antechamber limitation on molecule size (Thu Nov 01 2012 - 01:17:29 PDT)
Giulia
- Re: [AMBER] mmpbsa restart (Wed Nov 14 2012 - 08:14:09 PST)
- [AMBER] mmpbsa restart (Wed Nov 14 2012 - 04:31:18 PST)
Gustavo Seabra
- Re: [AMBER] WARNING: a parameter is 0.0 for atom (Fri Nov 16 2012 - 03:19:46 PST)
- Re: [AMBER] WARNING: a parameter is 0.0 for atom (Fri Nov 16 2012 - 02:51:16 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 (Thu Nov 15 2012 - 06:33:14 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 (Wed Nov 14 2012 - 10:41:51 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 (Wed Nov 14 2012 - 04:40:30 PST)
- Re: [AMBER] Best atom types for N-Oxides compounds like TMAO (Thu Nov 01 2012 - 07:22:00 PDT)
- Re: [AMBER] Best atom types for N-Oxides compounds like TMAO (Thu Nov 01 2012 - 06:49:37 PDT)
hari krishna
- Re: [AMBER] Problem in running parallel (Wed Oct 31 2012 - 23:13:52 PDT)
Hirdesh Kumar
- Re: [AMBER] Ligand appears broken after minimization (Wed Nov 28 2012 - 00:14:07 PST)
- [AMBER] Xleap rotation in mac OS (Tue Nov 27 2012 - 00:47:51 PST)
Ignacio J. General
- Re: [AMBER] Doubt about binding dissociation constant (Wed Nov 28 2012 - 10:56:57 PST)
Ilyas Yildirim
- Re: [AMBER] tleap not recognizing Na+ (Mon Nov 05 2012 - 10:59:25 PST)
InSuk Joung
- Re: [AMBER] Doubt about binding dissociation constant (Wed Nov 28 2012 - 10:18:42 PST)
Ismail, Mohd F.
- Re: [AMBER] INTER-molecular RDF only ? (Fri Nov 23 2012 - 14:09:58 PST)
- Re: [AMBER] INTER-molecular RDF only ? (Fri Nov 23 2012 - 12:34:31 PST)
- Re: [AMBER] COM removed message and Energy Drift (Thu Nov 15 2012 - 09:46:16 PST)
- Re: [AMBER] COM removed message and Energy Drift (Wed Nov 14 2012 - 12:50:26 PST)
- [AMBER] COM removed message and Energy Drift (Wed Nov 14 2012 - 12:38:41 PST)
- Re: [AMBER] Dipole from a mask (Fri Nov 09 2012 - 13:16:26 PST)
- Re: [AMBER] Dipole from a mask (Thu Nov 08 2012 - 21:13:15 PST)
- Re: [AMBER] Dipole from a mask (Thu Nov 08 2012 - 21:07:34 PST)
- Re: [AMBER] Dipole from a mask (Wed Nov 07 2012 - 14:26:56 PST)
- [AMBER] Dipole from a mask (Mon Nov 05 2012 - 13:29:34 PST)
Itamar Kass
- [AMBER] What nonbonded interactions cutoff to use in amber. (Sun Nov 25 2012 - 18:57:38 PST)
Jacopo Sgrignani
- Re: [AMBER] strange deprotonation in QM/MM (Thu Nov 22 2012 - 02:40:48 PST)
- [AMBER] strange deprotonation in QM/MM (Wed Nov 21 2012 - 07:17:07 PST)
- Re: [AMBER] WARNING: a parameter is 0.0 for atom (Fri Nov 16 2012 - 03:07:31 PST)
- [AMBER] WARNING: a parameter is 0.0 for atom (Fri Nov 16 2012 - 01:51:09 PST)
Jagur Lambix
- [AMBER] Polarizable force field for protein + ligand system (Tue Nov 27 2012 - 14:47:01 PST)
- [AMBER] simulation for a protein + ligand system with polarizable force field (Tue Nov 27 2012 - 12:44:20 PST)
JAIME RUBIO MARTINEZ
- [AMBER] references ? (Thu Nov 01 2012 - 11:27:40 PDT)
Jason Swails
- Re: [AMBER] Porcupine_Plots_Script (Fri Nov 30 2012 - 06:33:35 PST)
- Re: [AMBER] GPU compile TEST does not work. (Fri Nov 30 2012 - 05:02:46 PST)
- Re: [AMBER] is there a difference between the GTX 680 GPU's (Thu Nov 29 2012 - 16:35:40 PST)
- Re: [AMBER] is there a difference between the GTX 680 GPU's (Thu Nov 29 2012 - 15:19:58 PST)
- Re: [AMBER] sander.MPI (Thu Nov 29 2012 - 07:04:34 PST)
- Re: [AMBER] Compiler for Amber12 with GTX680 (Thu Nov 29 2012 - 05:37:32 PST)
- Re: [AMBER] sander.MPI (Thu Nov 29 2012 - 05:36:11 PST)
- Re: [AMBER] Solvation in Amber (Thu Nov 29 2012 - 04:52:37 PST)
- Re: [AMBER] Porcupine_Plots_Script (Thu Nov 29 2012 - 04:29:24 PST)
- Re: [AMBER] sander.MPI (Thu Nov 29 2012 - 03:40:14 PST)
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop -rdparm: a parameter array overflowed (Wed Nov 28 2012 - 07:23:58 PST)
- Re: [AMBER] calculate the binding free energy of more than one ligand in MMPBSA (Tue Nov 27 2012 - 09:33:28 PST)
- Re: [AMBER] Porcupine_Plots_Script (Tue Nov 27 2012 - 07:25:29 PST)
- Re: [AMBER] Problem to run sander with more than 60 atom types (Tue Nov 27 2012 - 06:59:48 PST)
- Re: [AMBER] Problem to run sander with more than 60 atom types (Tue Nov 27 2012 - 05:29:38 PST)
- Re: [AMBER] complete bond energy list (Tue Nov 27 2012 - 05:27:01 PST)
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop (Tue Nov 27 2012 - 04:54:39 PST)
- Re: [AMBER] Xleap rotation in mac OS (Tue Nov 27 2012 - 04:28:22 PST)
- Re: [AMBER] What nonbonded interactions cutoff to use in amber. (Mon Nov 26 2012 - 05:52:52 PST)
- Re: [AMBER] selecting a gpu device in multiple gpu system (Wed Nov 21 2012 - 06:35:54 PST)
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' (Tue Nov 20 2012 - 06:38:42 PST)
- Re: [AMBER] generate rst from mdcrd (Mon Nov 19 2012 - 12:49:08 PST)
- Re: [AMBER] mixing of scaling factor in amber 12 (Mon Nov 19 2012 - 05:27:44 PST)
- Re: [AMBER] Antechamber (Sat Nov 17 2012 - 12:42:39 PST)
- Re: [AMBER] Theorical ramachandran map/energy map of modified residues (Fri Nov 16 2012 - 11:11:50 PST)
- Re: [AMBER] Error in script file while running mm_pbsa.pl (Fri Nov 16 2012 - 04:58:55 PST)
- Re: [AMBER] Problem with the specification of the bellymask (Thu Nov 15 2012 - 18:18:40 PST)
- Re: [AMBER] Energy Analysis from Trajectory (Thu Nov 15 2012 - 08:26:02 PST)
- Re: [AMBER] COM removed message and Energy Drift (Thu Nov 15 2012 - 04:36:18 PST)
- Re: [AMBER] mmpbsa restart (Wed Nov 14 2012 - 08:33:09 PST)
- Re: [AMBER] mmpbsa restart (Wed Nov 14 2012 - 05:18:49 PST)
- Re: [AMBER] Explicit 1-4 pairs (Wed Nov 14 2012 - 05:17:35 PST)
- Re: [AMBER] MM PBSA error calculating entropy (Tue Nov 13 2012 - 14:55:05 PST)
- Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj (Tue Nov 13 2012 - 06:00:20 PST)
- Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj (Tue Nov 13 2012 - 05:36:35 PST)
- Re: [AMBER] cppparmstrip command provokes segmentation fault (Tue Nov 13 2012 - 05:34:26 PST)
- Re: [AMBER] Amber Error : Segmentation fault (Mon Nov 12 2012 - 04:25:09 PST)
- Re: [AMBER] System blows up after several nanoseconds using Amber 12 (Sat Nov 10 2012 - 08:13:14 PST)
- Re: [AMBER] System blows up after several nanoseconds using Amber 12 (Fri Nov 09 2012 - 20:34:26 PST)
- Re: [AMBER] EHBOND values and RESTRAINT values in mdout file (Fri Nov 09 2012 - 07:02:55 PST)
- Re: [AMBER] Error at the end of entropy calculation via MMPBSA.py (Fri Nov 09 2012 - 07:01:35 PST)
- Re: [AMBER] EHBOND values and RESTRAINT values in mdout file (Thu Nov 08 2012 - 15:16:33 PST)
- Re: [AMBER] AmberTools versions (Thu Nov 08 2012 - 12:36:56 PST)
- Re: [AMBER] Multi-protein simulation in a box (Thu Nov 08 2012 - 08:30:19 PST)
- Re: [AMBER] genMetalFF.sh and getCharges.sh not exist (Thu Nov 08 2012 - 05:27:25 PST)
- Re: [AMBER] compiler errors (Thu Nov 08 2012 - 04:57:05 PST)
- Re: [AMBER] best tutorials (Wed Nov 07 2012 - 15:38:53 PST)
- Re: [AMBER] NAMD failed to read Amber parm file (Wed Nov 07 2012 - 11:19:55 PST)
- Re: [AMBER] error of MMPBSA calculation using the prmtop and inpcrd generated by Chamber program (Wed Nov 07 2012 - 11:16:19 PST)
- Re: [AMBER] Energy Analysis from Trajectory (Wed Nov 07 2012 - 11:10:21 PST)
- Re: [AMBER] questions about AMBER prep files (Tue Nov 06 2012 - 14:38:47 PST)
- Re: [AMBER] questions about thermodynamic integration atom name and order (Tue Nov 06 2012 - 14:14:31 PST)
- Re: [AMBER] compiler errors (Tue Nov 06 2012 - 09:03:51 PST)
- Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE (Tue Nov 06 2012 - 07:50:52 PST)
- Re: [AMBER] Cannot match namelist object name scee (Tue Nov 06 2012 - 07:10:42 PST)
- Re: [AMBER] MMPBSA.py "timer: need to reset the time before start" (Mon Nov 05 2012 - 10:04:23 PST)
- Re: [AMBER] Problem related to RMSD (Sun Nov 04 2012 - 17:35:40 PST)
- Re: [AMBER] no leaprc in search path (Sun Nov 04 2012 - 08:40:49 PST)
- Re: [AMBER] no leaprc in search path (Sun Nov 04 2012 - 07:14:31 PST)
- Re: [AMBER] Problem related to the RMSD (Sat Nov 03 2012 - 08:43:20 PDT)
- Re: [AMBER] how to calculate binding energy of one receptor and two ligands? (Fri Nov 02 2012 - 21:42:05 PDT)
- Re: [AMBER] how to calculate binding energy of one receptor and two ligands? (Fri Nov 02 2012 - 09:37:17 PDT)
Jia Xu
- Re: [AMBER] Porcupine_Plots_Script (Mon Nov 26 2012 - 10:18:07 PST)
- [AMBER] Porcupine_Plots_Script (Mon Nov 26 2012 - 03:17:45 PST)
- Re: [AMBER] genMetalFF.sh and getCharges.sh not exist (Thu Nov 08 2012 - 09:42:25 PST)
- [AMBER] genMetalFF.sh and getCharges.sh not exist (Wed Nov 07 2012 - 23:17:07 PST)
Jiri Sponer
- [AMBER] postdoc RNA/DNA computations (Tue Nov 27 2012 - 04:50:23 PST)
Jitesh Doshi
- Re: [AMBER] Ligand appears broken after minimization (Tue Nov 27 2012 - 22:04:25 PST)
- [AMBER] Ligand appears broken after minimization (Wed Nov 21 2012 - 01:49:15 PST)
Joakim Jämbeck
- [AMBER] Explicit 1-4 pairs (Wed Nov 14 2012 - 02:09:39 PST)
Jodi Ann Hadden
- Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE (Tue Nov 06 2012 - 08:23:59 PST)
Jonathan Gough
- Re: [AMBER] is there a difference between the GTX 680 GPU's (Thu Nov 29 2012 - 18:41:34 PST)
- Re: [AMBER] is there a difference between the GTX 680 GPU's (Thu Nov 29 2012 - 18:06:37 PST)
- Re: [AMBER] is there a difference between the GTX 680 GPU's (Thu Nov 29 2012 - 16:17:07 PST)
- [AMBER] is there a difference between the GTX 680 GPU's (Thu Nov 29 2012 - 14:03:34 PST)
João Ribeiro
- Re: [AMBER] Calculating volume of the ligand (Wed Nov 28 2012 - 07:43:51 PST)
Kepa K. Burusco
- Re: [AMBER] Energy Analysis from Trajectory (Thu Nov 15 2012 - 08:21:05 PST)
- Re: [AMBER] Energy Analysis from Trajectory (Wed Nov 14 2012 - 13:54:09 PST)
klechward.wp.pl
- [AMBER] Odp: Re: problem for lipid GAFF (Wed Nov 14 2012 - 01:28:19 PST)
Krisztina Feher
- Re: [AMBER] bond missing in phosphate group after antechamber run (Thu Nov 08 2012 - 08:55:45 PST)
- Re: [AMBER] bond missing in phosphate group after antechamber run (Thu Nov 08 2012 - 05:27:04 PST)
- Re: [AMBER] bond missing in phosphate group after antechamber run (Wed Nov 07 2012 - 13:55:48 PST)
- [AMBER] bond missing in phosphate group after antechamber run (Wed Nov 07 2012 - 11:00:38 PST)
Kshatresh Dutta Dubey
- Re: [AMBER] Ligand appears broken after minimization (Wed Nov 21 2012 - 01:56:54 PST)
kurisaki
- Re: [AMBER] GPU compile TEST does not work. (Fri Nov 30 2012 - 06:07:25 PST)
- Re: [AMBER] GPU compile TEST does not work. (Thu Nov 29 2012 - 23:06:13 PST)
- [AMBER] GPU compile TEST does not work. (Thu Nov 29 2012 - 21:09:33 PST)
- Re: [AMBER] Compiler for Amber12 with GTX680 (Thu Nov 29 2012 - 05:58:05 PST)
- [AMBER] Compiler for Amber12 with GTX680 (Thu Nov 29 2012 - 02:46:24 PST)
Liu Denis
- Re: [AMBER] Can I mix Glycam and Gaff in a small molecule? (Tue Nov 20 2012 - 16:49:28 PST)
- [AMBER] Can I mix Glycam and Gaff in a small molecule? (Sun Nov 18 2012 - 23:01:37 PST)
- Re: [AMBER] How to use q4md-CD? (Tue Nov 06 2012 - 01:51:18 PST)
- [AMBER] How to use q4md-CD? (Mon Nov 05 2012 - 08:07:55 PST)
manikanthan bhavaraju
- Re: [AMBER] Doubt about binding dissociation constant (Wed Nov 28 2012 - 10:29:39 PST)
- [AMBER] Doubt about binding dissociation constant (Wed Nov 28 2012 - 10:05:59 PST)
- Re: [AMBER] Calculating volume of the ligand (Wed Nov 28 2012 - 07:51:54 PST)
- [AMBER] Calculating volume of the ligand (Wed Nov 28 2012 - 06:30:15 PST)
- Re: [AMBER] problem with Ca2.lib (Wed Nov 07 2012 - 12:04:05 PST)
- [AMBER] problem with Ca2.lib (Wed Nov 07 2012 - 11:28:50 PST)
marawan hussain
- [AMBER] AMBER-ORCA-Freq (Thu Nov 15 2012 - 14:13:25 PST)
- [AMBER] AMBER-ORCA (Wed Nov 14 2012 - 23:51:55 PST)
- [AMBER] AMBER/ORCA (Wed Nov 14 2012 - 19:18:19 PST)
- [AMBER] AMBER-Gaussian and Infrared (Fri Nov 02 2012 - 19:07:05 PDT)
Marc van der Kamp
- Re: [AMBER] selecting a gpu device in multiple gpu system (Wed Nov 21 2012 - 03:02:39 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 (Wed Nov 14 2012 - 12:46:59 PST)
Marek Maly
- Re: [AMBER] is there a difference between the GTX 680 GPU's (Thu Nov 29 2012 - 18:16:47 PST)
- Re: [AMBER] is there a difference between the GTX 680 GPU's (Thu Nov 29 2012 - 16:44:58 PST)
- Re: [AMBER] is there a difference between the GTX 680 GPU's (Thu Nov 29 2012 - 16:13:19 PST)
- Re: [AMBER] INTER-molecular RDF only ? (Fri Nov 23 2012 - 14:35:59 PST)
- Re: [AMBER] INTER-molecular RDF only ? (Fri Nov 23 2012 - 13:13:53 PST)
- [AMBER] INTER-molecular RDF only ? (Fri Nov 23 2012 - 05:22:09 PST)
- Re: [AMBER] about angle restraint (Tue Nov 06 2012 - 16:21:32 PST)
Mark Zottola
- [AMBER] Generating a solvent Box from organic solvent (Mon Nov 12 2012 - 16:48:24 PST)
Maxier Acosta Santiago
- [AMBER] Forcefield (Wed Nov 21 2012 - 12:06:12 PST)
- Re: [AMBER] Antechamber (Sun Nov 18 2012 - 08:20:37 PST)
- [AMBER] Antechamber (Sat Nov 17 2012 - 12:06:32 PST)
- [AMBER] AmberTools versions (Thu Nov 08 2012 - 12:05:15 PST)
Maximilian Ebert
- Re: [AMBER] Heme iron definition: Atom type missing (Fri Nov 09 2012 - 22:27:18 PST)
- Re: [AMBER] Heme iron definition: Atom type missing (Fri Nov 09 2012 - 11:59:28 PST)
- [AMBER] Heme iron definition: Atom type missing (Thu Nov 08 2012 - 05:35:28 PST)
- Re: [AMBER] Amber and P450 cytochromes (Thu Nov 01 2012 - 08:25:07 PDT)
Meli Massimiliano
- Re: [AMBER] NOE calculation (Tue Nov 13 2012 - 08:14:38 PST)
- [AMBER] NOE calculation (Tue Nov 13 2012 - 02:26:33 PST)
Miguel Ortiz Lombardia
- Re: [AMBER] Problem related to RMSD (Sun Nov 04 2012 - 23:19:21 PST)
Miguel Ortiz Lombardía
- [AMBER] Error at the end of entropy calculation via MMPBSA.py (Fri Nov 09 2012 - 06:31:00 PST)
monica.imtech.res.in
- Re: [AMBER] Porcupine_Plots_Script (Fri Nov 30 2012 - 06:19:13 PST)
- Re: [AMBER] Porcupine_Plots_Script (Thu Nov 29 2012 - 04:08:00 PST)
- Re: [AMBER] Porcupine_Plots_Script (Tue Nov 27 2012 - 07:18:38 PST)
- Re: [AMBER] Porcupine_Plots_Script (Mon Nov 26 2012 - 04:11:36 PST)
Niel Henriksen
- Re: [AMBER] Problem related to RMSD (Sun Nov 04 2012 - 20:20:02 PST)
- Re: [AMBER] Problem related to RMSD (Sun Nov 04 2012 - 09:57:53 PST)
- Re: [AMBER] Problem related to the RMSD (Sun Nov 04 2012 - 06:52:15 PST)
Osman, Roman
- [AMBER] residuegen (Wed Nov 14 2012 - 14:59:52 PST)
Pecher, Josua
- Re: [AMBER] different force fields for different molecules in leap (Thu Nov 08 2012 - 08:25:29 PST)
- [AMBER] different force fields for different molecules in leap (Thu Nov 08 2012 - 08:04:04 PST)
Pyle, Ronald
- Re: [AMBER] EHBOND values and RESTRAINT values in mdout file (Fri Nov 09 2012 - 06:13:27 PST)
- [AMBER] EHBOND values and RESTRAINT values in mdout file (Thu Nov 08 2012 - 14:55:13 PST)
rahul sarma
- Re: [AMBER] trajout command in ptraj (Mon Nov 19 2012 - 20:14:01 PST)
- [AMBER] trajout command in ptraj (Sun Nov 18 2012 - 23:52:48 PST)
Rajeswari A.
- Re: [AMBER] Multi-protein simulation in a box (Thu Nov 08 2012 - 23:08:07 PST)
- [AMBER] Multi-protein simulation in a box (Thu Nov 08 2012 - 01:28:04 PST)
Ravi Tripathi
- Re: [AMBER] Solvation in Amber (Fri Nov 30 2012 - 02:02:09 PST)
- [AMBER] Solvation in Amber (Thu Nov 29 2012 - 03:46:42 PST)
- Re: [AMBER] Antechamber - Problem with protonated oxygen (Tue Nov 27 2012 - 22:20:31 PST)
- Re: [AMBER] Antechamber-- Creating inputs for Ammonium-Borane (Tue Nov 27 2012 - 21:59:12 PST)
- [AMBER] Antechamber - Problem with protonated oxygen (Tue Nov 27 2012 - 21:58:39 PST)
- [AMBER] Antechamber-- Creating inputs for Ammonium-Borane (Tue Nov 27 2012 - 02:09:31 PST)
Ray Luo
- Re: [AMBER] The differences of MMPBSA calculations between AT1.5 and AT12, especially in PBSA solvation model. (Thu Nov 29 2012 - 19:24:28 PST)
Ray Luo, Ph.D.
- Re: [AMBER] 回复: Re: The differences of MMPBSA calculations between AT1.5and AT12, especially in PBSA solvation model. (Fri Nov 30 2012 - 09:28:55 PST)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE (Fri Nov 16 2012 - 15:46:12 PST)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE (Wed Nov 14 2012 - 21:17:44 PST)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE (Wed Nov 14 2012 - 10:08:27 PST)
- Re: [AMBER] No radius found for Mg+ using mm_pbsa.pl script (Fri Nov 09 2012 - 09:48:50 PST)
- Re: [AMBER] solvation free enrgy calculation using PB equation. (Thu Nov 01 2012 - 10:31:24 PDT)
Robert Konecny
- Re: [AMBER] large value of "fglen" and "cglen"of iAPBS initiation during MMPBSA python script calculation (Thu Nov 15 2012 - 21:08:27 PST)
Roitberg,Adrian E
- Re: [AMBER] System blows up after several nanoseconds using Amber 12 (Sat Nov 10 2012 - 09:06:10 PST)
- Re: [AMBER] System blows up after several nanoseconds using Amber 12 (Sat Nov 10 2012 - 07:37:48 PST)
- Re: [AMBER] Umbrella sampling with pmemd (Wed Nov 07 2012 - 07:03:25 PST)
- Re: [AMBER] Umbrella sampling with pmemd (Tue Nov 06 2012 - 23:03:34 PST)
- Re: [AMBER] Energy Analysis from Trajectory (Tue Nov 06 2012 - 22:09:14 PST)
Romelia Salomon
- Re: [AMBER] questions about Accelerated MD (Mon Nov 19 2012 - 13:47:10 PST)
- Re: [AMBER] questions about Accelerated MD (Mon Nov 19 2012 - 10:20:25 PST)
- Re: [AMBER] questions about Accelerated MD (Mon Nov 19 2012 - 08:35:36 PST)
Ross Walker
- Re: [AMBER] is there a difference between the GTX 680 GPU's (Thu Nov 29 2012 - 18:31:44 PST)
- Re: [AMBER] is there a difference between the GTX 680 GPU's (Thu Nov 29 2012 - 16:58:33 PST)
- Re: [AMBER] GPU and ntpr (Tue Nov 27 2012 - 10:48:13 PST)
- Re: [AMBER] GPU and ntpr (Fri Nov 23 2012 - 17:27:29 PST)
- Re: [AMBER] selecting a gpu device in multiple gpu system (Wed Nov 21 2012 - 10:09:35 PST)
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' (Wed Nov 21 2012 - 10:03:22 PST)
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' (Tue Nov 20 2012 - 14:14:55 PST)
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' (Tue Nov 20 2012 - 13:21:23 PST)
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' (Tue Nov 20 2012 - 13:09:36 PST)
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' (Tue Nov 20 2012 - 08:28:01 PST)
- Re: [AMBER] Kepler II (K20) benchmark results? (Thu Nov 15 2012 - 16:42:57 PST)
- Re: [AMBER] problem for lipid GAFF (Wed Nov 14 2012 - 09:36:21 PST)
- Re: [AMBER] problem for lipid GAFF (Tue Nov 13 2012 - 10:23:25 PST)
- Re: [AMBER] problem for lipid GAFF (Tue Nov 13 2012 - 09:03:32 PST)
- Re: [AMBER] Urgent (Sun Nov 11 2012 - 23:26:41 PST)
- Re: [AMBER] Amber Error : Segmentation fault (Sun Nov 11 2012 - 22:33:17 PST)
- Re: [AMBER] pmemd cuda MPI nmropt crashes (Mon Nov 05 2012 - 23:12:55 PST)
- Re: [AMBER] pmemd cuda MPI nmropt crashes (Mon Nov 05 2012 - 21:44:19 PST)
- Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE (Mon Nov 05 2012 - 21:38:58 PST)
- Re: [AMBER] pmemd cuda MPI nmropt crashes (Mon Nov 05 2012 - 21:29:08 PST)
- Re: [AMBER] workstation (Mon Nov 05 2012 - 12:39:26 PST)
- Re: [AMBER] vlimit exceeded error regarding (Fri Nov 02 2012 - 09:21:50 PDT)
- Re: [AMBER] vlimit exceed for step 1- regarding (Thu Nov 01 2012 - 22:32:37 PDT)
- Re: [AMBER] Amber12 PETASCALE Benchmarking. (Thu Nov 01 2012 - 22:27:54 PDT)
sa
- Re: [AMBER] Best atom types for N-Oxides compounds like TMAO (Thu Nov 01 2012 - 07:30:09 PDT)
- Re: [AMBER] Best atom types for N-Oxides compounds like TMAO (Thu Nov 01 2012 - 07:05:40 PDT)
- [AMBER] Best atom types for N-Oxides compounds like TMAO (Thu Nov 01 2012 - 05:39:44 PDT)
Sajeewa Pemasinghe
- Re: [AMBER] Problem with the specification of the bellymask (Thu Nov 15 2012 - 19:39:38 PST)
- [AMBER] Problem with the specification of the bellymask (Thu Nov 15 2012 - 16:55:38 PST)
- Re: [AMBER] Umbrella sampling with pmemd (Tue Nov 06 2012 - 23:30:05 PST)
- [AMBER] Umbrella sampling with pmemd (Tue Nov 06 2012 - 22:59:17 PST)
- Re: [AMBER] Clarifications in umbrella sampling (Mon Nov 05 2012 - 06:06:02 PST)
- Re: [AMBER] Clarifications in umbrella sampling (Sun Nov 04 2012 - 23:28:03 PST)
- [AMBER] Clarifications in umbrella sampling (Sun Nov 04 2012 - 20:32:22 PST)
Sangeetha B
- [AMBER] imaging issues during RMSF (Fri Nov 30 2012 - 06:16:52 PST)
Sangmin Lee
- [AMBER] Obtain trajectory coordinates from LMOD minimization (Thu Nov 08 2012 - 22:23:57 PST)
Sanjib Paul
- Re: [AMBER] Download problem of amber12 (Thu Nov 01 2012 - 03:59:43 PDT)
Sarah Edwards
- [AMBER] LMOD issues in Amber 12 (Mon Nov 26 2012 - 11:05:39 PST)
Sasha Perkins
- Re: [AMBER] System blows up after several nanoseconds using Amber 12 (Sat Nov 10 2012 - 09:02:17 PST)
- Re: [AMBER] System blows up after several nanoseconds using Amber 12 (Sat Nov 10 2012 - 07:32:45 PST)
- [AMBER] System blows up after several nanoseconds using Amber 12 (Fri Nov 09 2012 - 19:19:40 PST)
Scott Brozell
- Re: [AMBER] pmemd cuda MPI nmropt crashes (Wed Nov 07 2012 - 09:44:45 PST)
- Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE (Wed Nov 07 2012 - 09:25:13 PST)
- Re: [AMBER] pmemd cuda MPI nmropt crashes (Wed Nov 07 2012 - 08:55:13 PST)
- Re: [AMBER] pmemd cuda MPI nmropt crashes (Mon Nov 05 2012 - 22:36:36 PST)
- [AMBER] pmemd cuda MPI and PBS_GPUFILE (Mon Nov 05 2012 - 22:24:45 PST)
- [AMBER] pmemd cuda MPI nmropt crashes (Mon Nov 05 2012 - 22:08:45 PST)
Scott Le Grand
- Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE (Wed Nov 07 2012 - 09:52:20 PST)
- Re: [AMBER] pmemd cuda MPI nmropt crashes (Tue Nov 06 2012 - 10:04:09 PST)
- Re: [AMBER] pmemd cuda MPI nmropt crashes (Tue Nov 06 2012 - 05:47:31 PST)
setyanto md
- [AMBER] Cannot setting AMBERHOME on ubuntu 12.04 (Fri Nov 02 2012 - 01:14:58 PDT)
Sharma, Purshotam
- [AMBER] C-C-N angle parameters for benzonitrile (Fri Nov 16 2012 - 11:07:48 PST)
Shashidhar Rao
- Re: [AMBER] Reading DESMOND MD trajectory files in CPPTRAJ... (Tue Nov 27 2012 - 17:20:44 PST)
- [AMBER] Reading DESMOND MD trajectory files in CPPTRAJ... (Tue Nov 27 2012 - 13:14:49 PST)
Shubhadip Das
- [AMBER] problem in loading pdb in xleap (Fri Nov 30 2012 - 23:12:53 PST)
Shuyi Cao
- [AMBER] calculate the binding free energy of more than one ligand in MMPBSA (Tue Nov 27 2012 - 09:05:28 PST)
Sindrila Dutta banik
- [AMBER] Primary structur to 3D structure (Thu Nov 08 2012 - 11:18:29 PST)
- [AMBER] Problem related to the RMSD (Sun Nov 04 2012 - 22:37:27 PST)
- [AMBER] Problem related to RMSD (Sun Nov 04 2012 - 20:50:08 PST)
- [AMBER] Problem related to RMSD (Sun Nov 04 2012 - 19:57:44 PST)
- [AMBER] Problem related to RMSD (Sun Nov 04 2012 - 09:43:08 PST)
- [AMBER] Problem related to the RMSD (Sat Nov 03 2012 - 22:29:39 PDT)
- [AMBER] Problem related to the RMSD (Sat Nov 03 2012 - 07:25:11 PDT)
Sneha Menon
- [AMBER] NAMD failed to read Amber parm file (Wed Nov 07 2012 - 04:25:36 PST)
Souvik Sur
- [AMBER] Regarding RNA Duplex formation (Tue Nov 13 2012 - 22:50:26 PST)
- [AMBER] Regarding Quadruplex Formation (Fri Nov 09 2012 - 09:54:17 PST)
steinbrt.rci.rutgers.edu
- Re: [AMBER] Clarifications in umbrella sampling (Mon Nov 05 2012 - 00:20:01 PST)
Su, Shiquan
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' (Tue Nov 20 2012 - 13:04:18 PST)
- Re: [AMBER] Problem with "make install" after "./configure intel" (Tue Nov 13 2012 - 13:50:18 PST)
- Re: [AMBER] Problem with "make install" after "./configure intel" (Tue Nov 13 2012 - 13:37:08 PST)
- [AMBER] Problem with "make install" after "./configure intel" (Tue Nov 13 2012 - 13:16:33 PST)
subramanian boopathi
- [AMBER] error in heating process (Tue Nov 27 2012 - 21:47:54 PST)
- [AMBER] Heating process- amber 8 regarding (Thu Nov 22 2012 - 23:04:01 PST)
- [AMBER] vlimit exceeded error regarding (Fri Nov 02 2012 - 08:01:24 PDT)
- [AMBER] vlimit exceed for step 1- regarding (Thu Nov 01 2012 - 21:55:42 PDT)
- [AMBER] metal protein -regarding (Thu Nov 01 2012 - 03:49:52 PDT)
Subrata Paul
- Re: [AMBER] mixing of scaling factor in amber 12 (Mon Nov 19 2012 - 11:23:48 PST)
- [AMBER] mixing of scaling factor in amber 12 (Mon Nov 19 2012 - 00:56:58 PST)
Sumra Wajid Abbasi 30-FBAS/MSBI/F09
- Re: [AMBER] Amber Error : Segmentation fault (Mon Nov 12 2012 - 20:59:46 PST)
- Re: [AMBER] Amber Error : Segmentation fault (Mon Nov 12 2012 - 20:58:50 PST)
- Re: [AMBER] Amber Error : Segmentation fault (Mon Nov 12 2012 - 20:44:16 PST)
- Re: [AMBER] Amber Error : Segmentation fault (Mon Nov 12 2012 - 01:05:29 PST)
- Re: [AMBER] Amber Error : Segmentation fault (Sun Nov 11 2012 - 22:51:48 PST)
- [AMBER] Amber Error : Segmentation fault (Sun Nov 11 2012 - 22:15:16 PST)
Tan Yaw Sing
- Re: [AMBER] using nudged elastic band method with explicit solvent (Thu Nov 08 2012 - 18:57:18 PST)
- [AMBER] using nudged elastic band method with explicit solvent (Thu Nov 08 2012 - 02:48:00 PST)
- [AMBER] implementation of string method to find minimum free energy paths in Amber (Thu Nov 01 2012 - 06:49:34 PDT)
tec3.utah.edu
- Re: [AMBER] EHBOND values and RESTRAINT values in mdout file (Thu Nov 08 2012 - 15:25:04 PST)
Terry
- Re: [AMBER] Problem in running parallel (Wed Oct 31 2012 - 23:43:25 PDT)
Thomas Evangelidis
- Re: [AMBER] questions about Accelerated MD (Thu Nov 22 2012 - 13:47:22 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 07:46:38 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 06:47:43 PST)
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' (Tue Nov 20 2012 - 15:01:33 PST)
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' (Tue Nov 20 2012 - 13:31:44 PST)
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' (Tue Nov 20 2012 - 13:13:34 PST)
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' (Tue Nov 20 2012 - 12:47:55 PST)
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' (Tue Nov 20 2012 - 07:53:26 PST)
- [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' (Tue Nov 20 2012 - 01:50:52 PST)
- Re: [AMBER] questions about Accelerated MD (Mon Nov 19 2012 - 11:39:52 PST)
- Re: [AMBER] questions about Accelerated MD (Mon Nov 19 2012 - 08:46:54 PST)
- Re: [AMBER] questions about Accelerated MD (Sun Nov 18 2012 - 13:48:51 PST)
Tim Travers
- Re: [AMBER] problem with Ca2.lib (Wed Nov 07 2012 - 11:46:21 PST)
Vlad Cojocaru
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 07:52:13 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 07:35:20 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 06:51:53 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 06:21:38 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 06:13:45 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? (Wed Nov 21 2012 - 05:50:40 PST)
- Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj (Tue Nov 13 2012 - 06:11:29 PST)
- Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj (Tue Nov 13 2012 - 05:53:48 PST)
- Re: [AMBER] cppparmstrip command provokes segmentation fault (Tue Nov 13 2012 - 05:48:33 PST)
- [AMBER] cppparmstrip command provokes segmentation fault (Tue Nov 13 2012 - 04:13:55 PST)
- [AMBER] imaging namd-generated dcd trajectories with cpptraj (Tue Nov 13 2012 - 02:00:47 PST)
vojtech.mlynsky.upol.cz
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 (Thu Nov 15 2012 - 09:01:06 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 (Thu Nov 15 2012 - 05:08:15 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 (Wed Nov 14 2012 - 09:15:52 PST)
- [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 (Wed Nov 14 2012 - 03:05:29 PST)
Yi An
- Re: [AMBER] antechamber limitation on molecule size (Wed Nov 07 2012 - 19:07:40 PST)
Yulin Huang
- Re: [AMBER] questions about thermodynamic integration atom name and order (Wed Nov 07 2012 - 06:39:18 PST)
- Re: [AMBER] questions about AMBER prep files (Tue Nov 06 2012 - 14:43:11 PST)
- [AMBER] questions about AMBER prep files (Tue Nov 06 2012 - 14:14:43 PST)
- Re: [AMBER] questions about thermodynamic integration atom name and order (Tue Nov 06 2012 - 12:30:27 PST)
- Re: [AMBER] questions about thermodynamic integration atom name and order (Tue Nov 06 2012 - 07:20:32 PST)
Yunjie Zhao
- [AMBER] generate rst from mdcrd (Mon Nov 19 2012 - 11:57:04 PST)
יוכבד
- Re: [AMBER] complete bond energy list (Wed Nov 28 2012 - 00:41:29 PST)
- [AMBER] complete bond energy list (Tue Nov 27 2012 - 01:23:56 PST)
丁鹏飞
- [AMBER] calculation of protein-DNA complex structure (Mon Nov 26 2012 - 23:18:23 PST)
徐见容
- [AMBER] 回复: Re: The differences of MMPBSA calculations between AT1.5and AT12, especially in PBSA solvation model. (Thu Nov 29 2012 - 22:51:16 PST)
- [AMBER] The differences of MMPBSA calculations between AT1.5 andAT12, especially in PBSA solvation model. (Thu Nov 29 2012 - 19:05:52 PST)
- [AMBER] The differences of MMPBSA calculations between AT1.5 and AT12, especially in PBSA solvation model. (Thu Nov 29 2012 - 18:43:05 PST)
홍종희
- [AMBER] selecting a gpu device in multiple gpu system (Wed Nov 21 2012 - 02:42:38 PST)

Amber Archive Nov 2012 by author