Amber Archive Aug 2012: by subject

[AMBER] "QMMM of protein-ligand complex: Unable to achieve self consistency" and "bond stretch too far"
- psu4.uic.edu (Tue Aug 28 2012 - 16:48:31 PDT)
[AMBER] about ions
- Carlos Romero (Sun Aug 26 2012 - 16:55:19 PDT)
- Jason Swails (Fri Aug 24 2012 - 19:57:04 PDT)
- Carlos Romero (Fri Aug 24 2012 - 17:44:37 PDT)
- David A Case (Fri Aug 24 2012 - 05:52:28 PDT)
- Carlos Romero (Thu Aug 23 2012 - 22:50:34 PDT)
[AMBER] Accelerated Molecular Dynamics in Amber12
- Soumya Lipsa Rath (Mon Aug 20 2012 - 00:04:04 PDT)
- Ross Walker (Sun Aug 19 2012 - 23:06:13 PDT)
- Soumya Lipsa Rath (Sun Aug 19 2012 - 22:15:11 PDT)
[AMBER] Adding water molecules directly into files
- Marc van der Kamp (Wed Aug 29 2012 - 01:40:29 PDT)
- Jason Swails (Tue Aug 28 2012 - 21:24:58 PDT)
- Liu Denis (Tue Aug 28 2012 - 21:10:00 PDT)
- Adam Jion (Tue Aug 28 2012 - 21:04:15 PDT)
[AMBER] Amber 12 cuda test suite: some tests 'hang'
- Robert Crovella (Fri Aug 24 2012 - 06:58:32 PDT)
- Jan-Philip Gehrcke (Wed Aug 22 2012 - 14:11:31 PDT)
- Ross Walker (Wed Aug 22 2012 - 12:20:22 PDT)
- Jan-Philip Gehrcke (Wed Aug 22 2012 - 11:35:23 PDT)
- Ross Walker (Wed Aug 22 2012 - 09:04:14 PDT)
- Jan-Philip Gehrcke (Wed Aug 22 2012 - 08:57:02 PDT)
- Scott Le Grand (Wed Aug 22 2012 - 08:53:16 PDT)
- Jan-Philip Gehrcke (Wed Aug 22 2012 - 08:25:47 PDT)
- Ross Walker (Wed Aug 22 2012 - 08:08:47 PDT)
- Jan-Philip Gehrcke (Wed Aug 22 2012 - 08:00:35 PDT)
[AMBER] AMBER 12 Documentation detail missing
- Aron Broom (Tue Aug 07 2012 - 11:42:21 PDT)
[AMBER] amber 12 installation error
- Jason Swails (Thu Aug 23 2012 - 10:58:17 PDT)
- Shuyi Cao (Thu Aug 23 2012 - 09:04:22 PDT)
[AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander
- Ray Luo, Ph.D. (Fri Aug 31 2012 - 09:55:12 PDT)
- Jan-Philip Gehrcke (Fri Aug 31 2012 - 08:56:49 PDT)
- Jason Swails (Fri Aug 31 2012 - 08:43:24 PDT)
- Jan-Philip Gehrcke (Fri Aug 31 2012 - 07:58:31 PDT)
- Jason Swails (Fri Aug 31 2012 - 07:26:01 PDT)
- Jan-Philip Gehrcke (Fri Aug 31 2012 - 06:50:32 PDT)
- Jason Swails (Wed Aug 29 2012 - 07:17:17 PDT)
- Jan-Philip Gehrcke (Wed Aug 29 2012 - 05:11:28 PDT)
[AMBER] AMBER alanine scan with chlorine
- Bill Miller III (Tue Aug 21 2012 - 04:04:28 PDT)
- Mannan (Tue Aug 21 2012 - 02:31:50 PDT)
[AMBER] Amber force field for PNIPAM
- Vishal Maingi (Fri Aug 03 2012 - 03:25:18 PDT)
- Ganesh Kamath (Thu Aug 02 2012 - 16:36:10 PDT)
[AMBER] AMBER on GPU: What is the maximum no. of nodes tested?
- Scott Le Grand (Thu Aug 02 2012 - 08:00:08 PDT)
- Catein Catherine (Wed Aug 01 2012 - 03:40:19 PDT)
[AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland
- Albert (Fri Aug 24 2012 - 01:47:01 PDT)
- Ross Walker (Thu Aug 23 2012 - 11:16:35 PDT)
- Albert (Thu Aug 23 2012 - 11:08:16 PDT)
- Ross Walker (Thu Aug 23 2012 - 11:05:14 PDT)
[AMBER] amber10 install
- Qian Wang (Thu Aug 16 2012 - 07:33:16 PDT)
- David A Case (Thu Aug 16 2012 - 07:25:40 PDT)
- Qian Wang (Thu Aug 16 2012 - 07:18:40 PDT)
- case (Wed Aug 15 2012 - 18:22:58 PDT)
- Qian Wang (Wed Aug 15 2012 - 13:31:00 PDT)
[AMBER] amber10 install (mpi)
- Qian Wang (Wed Aug 22 2012 - 07:41:09 PDT)
- case (Tue Aug 21 2012 - 18:26:47 PDT)
- Jason Swails (Tue Aug 21 2012 - 16:20:43 PDT)
- Qian Wang (Tue Aug 21 2012 - 15:14:28 PDT)
- Jason Swails (Tue Aug 21 2012 - 15:05:40 PDT)
- Qian Wang (Tue Aug 21 2012 - 14:39:42 PDT)
- Jason Swails (Tue Aug 21 2012 - 14:18:50 PDT)
- Qian Wang (Tue Aug 21 2012 - 14:11:22 PDT)
[AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang
- Jason Swails (Thu Aug 30 2012 - 08:29:34 PDT)
- Yu Chen (Thu Aug 30 2012 - 08:19:17 PDT)
- Ben Roberts (Wed Aug 29 2012 - 15:54:50 PDT)
- Jason Swails (Wed Aug 29 2012 - 14:16:21 PDT)
- Yu Chen (Wed Aug 29 2012 - 13:26:56 PDT)
[AMBER] Amber12 parallel running issues
- Miguel Ortiz Lombardia (Mon Aug 06 2012 - 11:50:37 PDT)
- Prabu Manoharan (Mon Aug 06 2012 - 10:00:50 PDT)
[AMBER] angles and dihedrals for lone pairs
- case (Tue Aug 07 2012 - 18:52:12 PDT)
- Ivanov, Maxim (Tue Aug 07 2012 - 15:19:48 PDT)
- case (Mon Aug 06 2012 - 06:06:17 PDT)
- Ivanov, Maxim (Sun Aug 05 2012 - 16:39:47 PDT)
[AMBER] area per lipid popc membrane
- Dickson, Callum (Thu Aug 23 2012 - 02:12:14 PDT)
- Albert (Wed Aug 22 2012 - 22:52:19 PDT)
- jojartb.jgypk.u-szeged.hu (Wed Aug 22 2012 - 22:19:14 PDT)
- Benjamin D Madej (Wed Aug 22 2012 - 16:20:55 PDT)
- Fabrício Bracht (Wed Aug 22 2012 - 15:39:26 PDT)
- Benjamin D Madej (Wed Aug 22 2012 - 10:51:37 PDT)
- Fabrício Bracht (Tue Aug 21 2012 - 14:25:28 PDT)
[AMBER] Aspartate and Glutamate naming in PDB
- Carlos Simmerling (Tue Aug 07 2012 - 04:43:27 PDT)
- Zalikha Ibrahim (Mon Aug 06 2012 - 18:39:29 PDT)
- Carlos Simmerling (Mon Aug 06 2012 - 18:23:41 PDT)
- Zalikha Ibrahim (Mon Aug 06 2012 - 18:21:05 PDT)
[AMBER] Bacteriochlorophyll parameters from Ceccarelli et al.?
- Marc van der Kamp (Thu Aug 30 2012 - 08:33:32 PDT)
[AMBER] Calculating Energy of an atom selection
- Aron Broom (Fri Aug 17 2012 - 14:19:28 PDT)
[AMBER] Can electrostatic potential of GBSA be visualized?
- Liu Denis (Sat Aug 25 2012 - 06:28:49 PDT)
[AMBER] Can we use Ambertools analysis MD from GROMACS
- Pawel (Mon Aug 27 2012 - 05:47:58 PDT)
- Jason Swails (Mon Aug 27 2012 - 04:02:25 PDT)
- Acoot Brett (Mon Aug 27 2012 - 01:52:30 PDT)
[AMBER] Can we use autoimage of cpptraj in AMBER 12?
- Jason Swails (Tue Aug 28 2012 - 07:41:25 PDT)
- Catein Catherine (Tue Aug 28 2012 - 07:31:14 PDT)
[AMBER] charge derivation for simulations in organic solvents
- Dr. Vitaly V. G. Chaban (Mon Aug 06 2012 - 08:18:06 PDT)
- Dr. Vitaly V. G. Chaban (Mon Aug 06 2012 - 07:58:22 PDT)
- Igor Pochorovski (Mon Aug 06 2012 - 07:53:31 PDT)
[AMBER] COM coordinates
- Vishal Maingi (Tue Aug 21 2012 - 23:59:25 PDT)
- Daniel Roe (Tue Aug 21 2012 - 14:00:56 PDT)
- Vishal Maingi (Tue Aug 21 2012 - 02:12:39 PDT)
- Vishal Maingi (Fri Aug 17 2012 - 15:57:38 PDT)
[AMBER] CPPTRAJ hbond command
- Daniel Roe (Wed Aug 29 2012 - 09:50:32 PDT)
- Samuel Genheden (Wed Aug 29 2012 - 07:35:01 PDT)
[AMBER] cpptraj surf
- Jason Swails (Fri Aug 24 2012 - 10:42:25 PDT)
- George Tzotzos (Fri Aug 24 2012 - 09:52:46 PDT)
- Daniel Roe (Fri Aug 24 2012 - 09:32:36 PDT)
- George Tzotzos (Fri Aug 24 2012 - 09:21:22 PDT)
- Jason Swails (Fri Aug 24 2012 - 08:47:59 PDT)
- George Tzotzos (Fri Aug 24 2012 - 08:28:55 PDT)
- Daniel Roe (Fri Aug 24 2012 - 07:37:37 PDT)
- George Tzotzos (Fri Aug 24 2012 - 06:22:01 PDT)
[AMBER] cpptraj: autoimage + anchor works very well.
- Catein Catherine (Tue Jul 31 2012 - 20:23:37 PDT)
[AMBER] CPPTRAJ: Is it a program that requires a large memory?
- Daniel Roe (Mon Aug 27 2012 - 18:02:21 PDT)
- Jason Swails (Mon Aug 27 2012 - 03:59:52 PDT)
- Catein Catherine (Mon Aug 27 2012 - 00:06:42 PDT)
[AMBER] Decomposing the free energy contributions to the binding free energy
- Jason Swails (Tue Aug 28 2012 - 07:05:19 PDT)
- Deák Robert (Tue Aug 28 2012 - 03:12:03 PDT)
- Liu Denis (Mon Aug 27 2012 - 17:51:39 PDT)
- Deák Robert (Mon Aug 27 2012 - 12:52:12 PDT)
- Liu Denis (Mon Aug 27 2012 - 09:47:12 PDT)
- Deák Robert (Mon Aug 27 2012 - 00:55:17 PDT)
[AMBER] Diffenent EPB in MMPBSA result with
- Qin Cai (Fri Aug 31 2012 - 11:35:13 PDT)
- Qin Cai (Thu Aug 23 2012 - 10:21:24 PDT)
- Miguel Ortiz Lombardia (Wed Aug 22 2012 - 10:26:13 PDT)
- Liu Denis (Wed Aug 22 2012 - 10:18:45 PDT)
- Liu Denis (Wed Aug 22 2012 - 02:03:56 PDT)
[AMBER] Different Properties Value with Tesla vs GeForce GPUs
- Ismail, Mohd F. (Thu Aug 23 2012 - 10:40:50 PDT)
[AMBER] Diverging sander.MPI results according to core allocation
- Jason Swails (Fri Aug 03 2012 - 13:22:55 PDT)
- Bashford, Donald (Fri Aug 03 2012 - 12:12:10 PDT)
- Jason Swails (Thu Aug 02 2012 - 20:41:41 PDT)
[AMBER] Dummy atom and PMEMD
- David A Case (Fri Aug 31 2012 - 05:08:45 PDT)
- Ali M. Naserian-Nik (Fri Aug 31 2012 - 00:20:57 PDT)
- Jason Swails (Thu Aug 30 2012 - 13:05:11 PDT)
- Ali M. Naserian-Nik (Thu Aug 30 2012 - 12:21:08 PDT)
- Jason Swails (Thu Aug 30 2012 - 11:48:05 PDT)
- Ali M. Naserian-Nik (Thu Aug 30 2012 - 11:29:31 PDT)
- David A Case (Thu Aug 30 2012 - 10:04:53 PDT)
- Ali M. Naserian-Nik (Tue Aug 28 2012 - 22:57:06 PDT)
- case (Tue Aug 28 2012 - 17:35:08 PDT)
- Ali M. Naserian-Nik (Tue Aug 28 2012 - 07:21:57 PDT)
[AMBER] Error message in cpptraj when running at single node in supercomputer using mpirun
- Catein Catherine (Sun Aug 19 2012 - 23:57:23 PDT)
- Jason Swails (Sun Aug 19 2012 - 21:07:09 PDT)
- Catein Catherine (Sun Aug 19 2012 - 18:53:31 PDT)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
- case (Fri Aug 31 2012 - 15:38:57 PDT)
- Gabriel Jara (Fri Aug 31 2012 - 13:50:14 PDT)
- Brian Radak (Fri Aug 31 2012 - 07:50:06 PDT)
- Gabriel Jara (Fri Aug 31 2012 - 07:39:51 PDT)
[AMBER] Errors during minimization (rfree: Error decoding variable 1 3)
- Jason Swails (Fri Aug 10 2012 - 05:40:15 PDT)
- Terry (Fri Aug 10 2012 - 01:06:01 PDT)
- Zalikha Ibrahim (Fri Aug 10 2012 - 01:01:52 PDT)
[AMBER] Extreme large scale movement of a residue
- Acoot Brett (Mon Aug 06 2012 - 03:38:42 PDT)
[AMBER] failed to config serial amber 12 on IBM POWER7
- David A Case (Fri Aug 24 2012 - 06:09:10 PDT)
- Yubo Fan (Thu Aug 23 2012 - 23:40:45 PDT)
- Yubo Fan (Thu Aug 23 2012 - 09:49:52 PDT)
[AMBER] Fatal error (Could not read velocities) during heating
- Jason Swails (Wed Aug 15 2012 - 06:02:57 PDT)
- David A Case (Wed Aug 15 2012 - 05:00:34 PDT)
- Zalikha Ibrahim (Wed Aug 15 2012 - 02:09:51 PDT)
[AMBER] Flag for saving particular residues.
- case (Sun Aug 19 2012 - 08:18:01 PDT)
- HIMANSHU JOSHI (Sat Aug 18 2012 - 23:04:58 PDT)
[AMBER] frcmod and lib files fro Cadmium
- Kong, Ren (Wed Aug 01 2012 - 13:39:20 PDT)
- Mahendra B Thapa (Wed Aug 01 2012 - 13:08:54 PDT)
[AMBER] Fwd: meaning of "tolerance" in REMD
- Jason Swails (Thu Aug 16 2012 - 15:56:07 PDT)
- Niel Henriksen (Thu Aug 16 2012 - 14:46:53 PDT)
- Sajeewa Pemasinghe (Thu Aug 16 2012 - 14:38:43 PDT)
- Brian Radak (Thu Aug 16 2012 - 11:53:12 PDT)
- Sajeewa Pemasinghe (Thu Aug 16 2012 - 11:02:54 PDT)
[AMBER] GDP and MG parameters
- Vlad Cojocaru (Tue Aug 28 2012 - 11:42:22 PDT)
- FyD (Tue Aug 28 2012 - 09:17:17 PDT)
- Vlad Cojocaru (Tue Aug 28 2012 - 04:09:22 PDT)
- FyD (Tue Aug 28 2012 - 03:15:54 PDT)
- George M Giambasu (Mon Aug 27 2012 - 09:40:18 PDT)
- Vlad Cojocaru (Mon Aug 27 2012 - 01:21:56 PDT)
[AMBER] General question
- George Tzotzos (Tue Aug 14 2012 - 01:12:50 PDT)
- Gould, Ian R (Tue Aug 14 2012 - 01:06:37 PDT)
- Jason Swails (Mon Aug 13 2012 - 19:08:01 PDT)
- George Tzotzos (Mon Aug 13 2012 - 13:42:02 PDT)
[AMBER] group specification for different force constants for different groups
- Jason Swails (Wed Aug 29 2012 - 10:41:09 PDT)
- Sajeewa Pemasinghe (Wed Aug 29 2012 - 10:06:36 PDT)
[AMBER] Have any one used the Nmode to calculate the entropy?
- Matthew Tessier (Mon Aug 20 2012 - 08:42:43 PDT)
- Matthew Tessier (Thu Aug 09 2012 - 12:12:46 PDT)
- Jason Swails (Thu Aug 09 2012 - 10:35:03 PDT)
- Kong, Ren (Thu Aug 09 2012 - 09:59:26 PDT)
[AMBER] Help about the igb
- Elaine Cheung (Mon Aug 27 2012 - 08:22:50 PDT)
- Carlos Simmerling (Sat Aug 25 2012 - 04:55:27 PDT)
- Elaine Cheung (Wed Aug 22 2012 - 18:51:39 PDT)
- Carlos Simmerling (Wed Aug 22 2012 - 15:28:26 PDT)
- Elaine Cheung (Wed Aug 22 2012 - 11:56:44 PDT)
[AMBER] help about TMD
- David A Case (Tue Aug 28 2012 - 06:19:25 PDT)
- 燕燕朱 (Tue Aug 28 2012 - 05:10:49 PDT)
[AMBER] Help with ncsu_abmd flooding mode
- M. L. Dodson (Mon Aug 27 2012 - 14:05:12 PDT)
- Jason Swails (Mon Aug 27 2012 - 11:16:26 PDT)
- Fabrício Bracht (Mon Aug 27 2012 - 10:48:17 PDT)
- Brian Radak (Mon Aug 27 2012 - 09:08:15 PDT)
- Fabrício Bracht (Mon Aug 27 2012 - 08:17:00 PDT)
- Fabrício Bracht (Thu Aug 16 2012 - 14:15:09 PDT)
[AMBER] How can I get a average structure?
- Sanjib Paul (Tue Aug 28 2012 - 09:39:24 PDT)
- Daniel Roe (Tue Aug 28 2012 - 09:12:52 PDT)
- Sanjib Paul (Tue Aug 28 2012 - 08:33:41 PDT)
- Jason Swails (Tue Aug 28 2012 - 07:13:18 PDT)
- Sanjib Paul (Tue Aug 28 2012 - 07:05:47 PDT)
[AMBER] How to choose a particular region to minimization?
- Jason Swails (Fri Aug 31 2012 - 07:31:26 PDT)
- Thanh Binh NGUYEN (Fri Aug 31 2012 - 04:09:50 PDT)
- Marc van der Kamp (Fri Aug 31 2012 - 03:49:06 PDT)
- Thanh Binh NGUYEN (Thu Aug 30 2012 - 23:55:02 PDT)
[AMBER] How to combine RMSF profiles?
- Jason Swails (Wed Aug 29 2012 - 21:48:56 PDT)
- Catein Catherine (Wed Aug 29 2012 - 20:10:43 PDT)
- Carlos Simmerling (Wed Aug 29 2012 - 07:48:11 PDT)
- Jason Swails (Wed Aug 29 2012 - 07:38:46 PDT)
- Catein Catherine (Tue Aug 28 2012 - 22:49:05 PDT)
[AMBER] How to derive dihedral angle force constants by MCPB
- Ben Roberts (Wed Aug 22 2012 - 15:50:15 PDT)
- JiYuan Liu (Wed Aug 22 2012 - 01:20:28 PDT)
[AMBER] How to get the averaged structure of each cluster with cpptraj?
- Daniel Roe (Mon Aug 20 2012 - 06:41:47 PDT)
- Catein Catherine (Mon Aug 20 2012 - 00:01:14 PDT)
[AMBER] how to include derived charges in AMBER
- Sanjib Paul (Tue Jul 31 2012 - 23:52:02 PDT)
[AMBER] how to make a certain ionic concentration for the system?
- Kong, Ren (Thu Aug 09 2012 - 09:46:19 PDT)
- Kong, Ren (Thu Aug 09 2012 - 09:45:28 PDT)
- Aron Broom (Wed Aug 08 2012 - 12:27:48 PDT)
- Brian Radak (Wed Aug 08 2012 - 12:26:09 PDT)
- Kong, Ren (Wed Aug 08 2012 - 09:29:50 PDT)
[AMBER] how to predict time for MMPBSA decomp analysis
- Jiri Sponer (Tue Aug 21 2012 - 00:44:00 PDT)
- Soumya Lipsa Rath (Mon Aug 20 2012 - 22:57:54 PDT)
- vaibhav dixit (Mon Aug 20 2012 - 22:03:13 PDT)
- vaibhav dixit (Thu Aug 16 2012 - 08:59:49 PDT)
- Jason Swails (Thu Aug 16 2012 - 07:34:26 PDT)
- vaibhav dixit (Wed Aug 15 2012 - 22:45:23 PDT)
[AMBER] How to recover box information from pdb with truncated octahedron solvent?
- Liu Denis (Thu Aug 09 2012 - 21:24:03 PDT)
[AMBER] How to save Eigenvectors of modes using MMPBSA.py script?
- habi (Thu Aug 09 2012 - 10:36:46 PDT)
[AMBER] Installation of Amber11
- case (Sat Aug 11 2012 - 05:57:31 PDT)
- Meena Singh (Sat Aug 11 2012 - 03:32:49 PDT)
[AMBER] Installation problem of AmberTools of AMBER11
- David A Case (Fri Aug 31 2012 - 05:13:18 PDT)
- Sanjib Paul (Thu Aug 30 2012 - 21:43:04 PDT)
- Jason Swails (Thu Aug 30 2012 - 13:03:27 PDT)
- Sanjib Paul (Thu Aug 30 2012 - 11:58:38 PDT)
- Jason Swails (Thu Aug 30 2012 - 10:10:28 PDT)
- Sanjib Paul (Thu Aug 30 2012 - 09:33:45 PDT)
- Jason Swails (Thu Aug 30 2012 - 07:34:55 PDT)
- Sanjib Paul (Thu Aug 30 2012 - 06:17:47 PDT)
- David A Case (Thu Aug 30 2012 - 05:16:47 PDT)
- Sanjib Paul (Wed Aug 29 2012 - 23:01:30 PDT)
[AMBER] Internal energy linear increase with temperature
- David A Case (Mon Aug 13 2012 - 08:16:19 PDT)
- Binwu Zhao (Mon Aug 13 2012 - 08:01:19 PDT)
[AMBER] Internal energy linear increase with temperature (David A Case)
- David A Case (Mon Aug 20 2012 - 13:40:43 PDT)
- Binwu Zhao (Mon Aug 20 2012 - 12:56:02 PDT)
[AMBER] ions concenration
- Carlos Romero (Fri Aug 31 2012 - 10:13:16 PDT)
- Carlos Romero (Fri Aug 31 2012 - 08:40:00 PDT)
- Marek Maly (Fri Aug 31 2012 - 08:07:43 PDT)
- Daniel Sindhikara (Fri Aug 31 2012 - 07:32:39 PDT)
- Carlos Romero (Thu Aug 30 2012 - 18:30:17 PDT)
[AMBER] Is there any guide/tutorial/review to decide input format for MD based on system under consideration
- vaibhav dixit (Tue Aug 21 2012 - 22:46:34 PDT)
[AMBER] job in multiple GPUs
- Vijay Manickam Achari (Tue Aug 14 2012 - 21:41:40 PDT)
[AMBER] keeping parts of a protein virtually frozen in MD with pmemd
- Sajeewa Pemasinghe (Wed Aug 29 2012 - 11:28:53 PDT)
[AMBER] laptop GPU support
- Scott Le Grand (Thu Aug 02 2012 - 08:04:43 PDT)
- Benjamin D Madej (Wed Aug 01 2012 - 11:14:05 PDT)
- Jason Swails (Wed Aug 01 2012 - 05:29:10 PDT)
- Thomas Evangelidis (Wed Aug 01 2012 - 03:08:52 PDT)
[AMBER] large difference between MMGBSA and MMPBSA free energy
- Ray Luo, Ph.D. (Wed Aug 01 2012 - 14:45:45 PDT)
- Kong, Ren (Wed Aug 01 2012 - 13:45:36 PDT)
- Ray Luo, Ph.D. (Wed Aug 01 2012 - 12:38:44 PDT)
- Kong, Ren (Wed Aug 01 2012 - 12:26:02 PDT)
[AMBER] lipid params and paper
- Albert (Tue Aug 07 2012 - 05:11:51 PDT)
- Gould, Ian R (Tue Aug 07 2012 - 05:08:54 PDT)
[AMBER] loading of a mutant protein in XLEaP
- Jason Swails (Thu Aug 23 2012 - 07:33:55 PDT)
- gargi borgohai (Wed Aug 22 2012 - 23:32:57 PDT)
[AMBER] Looking for parameters
- FyD (Thu Aug 09 2012 - 09:54:38 PDT)
- Kat Russell (Tue Aug 07 2012 - 08:22:51 PDT)
[AMBER] Looking for parameters for a metal-organic compound
- Kat Russell (Thu Aug 02 2012 - 11:10:08 PDT)
[AMBER] make test query
- vaibhav dixit (Thu Aug 02 2012 - 02:40:39 PDT)
[AMBER] Making a complex
- David A Case (Thu Aug 02 2012 - 05:00:52 PDT)
- Saaz Sakrikar (Thu Aug 02 2012 - 04:00:49 PDT)
[AMBER] MBAR calculation
- Brian Radak (Thu Aug 16 2012 - 08:50:57 PDT)
- Liu Denis (Thu Aug 16 2012 - 08:33:21 PDT)
[AMBER] meaning of "tolerance" in REMD
- Sajeewa Pemasinghe (Wed Aug 15 2012 - 11:12:48 PDT)
[AMBER] MMPBSA, nonpolar solvation free energy inp=1 versus inp=2
- Vlad Cojocaru (Tue Aug 07 2012 - 22:45:05 PDT)
- Ray Luo, Ph.D. (Tue Aug 07 2012 - 15:22:58 PDT)
- Vlad Cojocaru (Tue Aug 07 2012 - 10:04:50 PDT)
[AMBER] MMPBSA.py gbsa unrecognized
- Jason Swails (Tue Aug 21 2012 - 21:44:32 PDT)
- E. Nihal Korkmaz (Tue Aug 21 2012 - 21:19:33 PDT)
[AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
- Ray Luo, Ph.D. (Tue Aug 07 2012 - 15:17:15 PDT)
- Ray Luo, Ph.D. (Tue Aug 07 2012 - 15:16:18 PDT)
- Ray Luo, Ph.D. (Tue Aug 07 2012 - 15:15:38 PDT)
- Vlad Cojocaru (Tue Aug 07 2012 - 07:58:25 PDT)
- Jason Swails (Tue Aug 07 2012 - 07:49:29 PDT)
- Vlad Cojocaru (Tue Aug 07 2012 - 07:32:57 PDT)
- Niel Henriksen (Tue Aug 07 2012 - 07:30:07 PDT)
- Jason Swails (Tue Aug 07 2012 - 07:21:39 PDT)
- Vlad Cojocaru (Tue Aug 07 2012 - 06:53:57 PDT)
- Jason Swails (Tue Aug 07 2012 - 06:34:54 PDT)
- Vlad Cojocaru (Tue Aug 07 2012 - 06:03:12 PDT)
[AMBER] More RMS fit
- George Tzotzos (Thu Aug 23 2012 - 05:28:05 PDT)
[AMBER] MPI version of Amber on CPU provide different results in each run
- Liu Denis (Tue Aug 28 2012 - 18:02:05 PDT)
- Mohammad Ashraf Bhuiyan (Tue Aug 28 2012 - 16:46:47 PDT)
[AMBER] mpi4py import error mesage is improvable
- Jason Swails (Wed Aug 29 2012 - 07:25:28 PDT)
- Jan-Philip Gehrcke (Wed Aug 29 2012 - 02:20:46 PDT)
[AMBER] myristoyl lipid11/12 (DMPC)
- Vishal Maingi (Tue Aug 07 2012 - 06:15:59 PDT)
- Vishal Maingi (Tue Aug 07 2012 - 01:48:36 PDT)
[AMBER] newbie question: simulating miRNA
- Niel Henriksen (Fri Aug 31 2012 - 12:53:59 PDT)
- David A Case (Fri Aug 31 2012 - 12:44:25 PDT)
- Niel Henriksen (Fri Aug 31 2012 - 08:47:10 PDT)
- Michiel de Hoon (Fri Aug 31 2012 - 07:30:25 PDT)
[AMBER] nmode - calculation of vibrational frequencies
- Svetlana Oard (Thu Aug 23 2012 - 09:53:09 PDT)
- case (Tue Aug 21 2012 - 18:39:40 PDT)
- Svetlana Oard (Fri Aug 17 2012 - 09:04:33 PDT)
[AMBER] non integer charge in antechamber generated mol2 file
- FyD (Mon Aug 13 2012 - 09:35:31 PDT)
- Raik Grünberg (Fri Aug 10 2012 - 20:43:02 PDT)
- Raik Grünberg (Fri Aug 10 2012 - 20:28:42 PDT)
- case (Fri Aug 10 2012 - 05:35:41 PDT)
- FyD (Thu Aug 09 2012 - 08:53:54 PDT)
- Raik Grünberg (Wed Aug 08 2012 - 10:41:14 PDT)
- case (Mon Aug 06 2012 - 18:28:13 PDT)
- Raik Grünberg (Sat Aug 04 2012 - 19:38:18 PDT)
- Raik Grünberg (Sat Aug 04 2012 - 17:32:59 PDT)
[AMBER] non polar solvation energy
- kirtana S (Wed Aug 01 2012 - 12:26:03 PDT)
[AMBER] NPT at high pressure
- Francesco Pietra (Wed Aug 22 2012 - 07:36:37 PDT)
- Jason Swails (Wed Aug 22 2012 - 07:19:46 PDT)
- Francesco Pietra (Wed Aug 22 2012 - 06:33:30 PDT)
[AMBER] NPT equilibration error: ASSERTion 'e' failed in nonbond_list.F90 at line 849
- Maria Minakova (Thu Aug 02 2012 - 12:11:17 PDT)
[AMBER] parallel constraints SMD
- e g (Fri Aug 24 2012 - 12:38:03 PDT)
- Jason Swails (Fri Aug 24 2012 - 08:51:19 PDT)
- e g (Fri Aug 24 2012 - 08:39:59 PDT)
[AMBER] parallel installation problem: Amber11+AmberTools1.4 on a linux cluster
- Jason Swails (Thu Aug 23 2012 - 18:08:05 PDT)
- Alfred Zheng (Thu Aug 23 2012 - 17:14:00 PDT)
[AMBER] parallel run error
- Jason Swails (Mon Aug 27 2012 - 03:52:14 PDT)
- najmul arfin (Sun Aug 26 2012 - 22:04:43 PDT)
[AMBER] Particles diffuse very far away from each other
- Jason Swails (Mon Aug 27 2012 - 23:12:40 PDT)
- ariana karakutuk (Mon Aug 27 2012 - 22:11:07 PDT)
[AMBER] pbsa: how to increase the sampling volume (grid dimensions)?
- Ray Luo (Wed Aug 22 2012 - 07:25:49 PDT)
- Jan-Philip Gehrcke (Mon Aug 20 2012 - 03:24:49 PDT)
[AMBER] pmemd.cuda and nmropt
- Ross Walker (Mon Aug 20 2012 - 14:20:50 PDT)
- Larry Olson (Mon Aug 20 2012 - 14:08:46 PDT)
[AMBER] polarizable force field
- 旭东肖 (Wed Aug 08 2012 - 18:18:18 PDT)
- Yong Duan (Wed Aug 08 2012 - 15:19:55 PDT)
- 旭东肖 (Wed Aug 08 2012 - 06:46:13 PDT)
[AMBER] PRMTOP TO PSF
- case (Wed Aug 15 2012 - 18:16:09 PDT)
- manikanthan bhavaraju (Wed Aug 15 2012 - 11:34:29 PDT)
[AMBER] problem for MMPBSA.py in AmberTools12
- zhenquan hu (Sun Aug 05 2012 - 23:48:40 PDT)
- Bill Miller III (Fri Aug 03 2012 - 07:17:10 PDT)
- zhenquan hu (Fri Aug 03 2012 - 06:49:15 PDT)
[AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5
- David A Case (Thu Aug 02 2012 - 07:41:59 PDT)
- Prabu Manoharan (Thu Aug 02 2012 - 05:48:32 PDT)
- David A Case (Wed Aug 01 2012 - 07:08:29 PDT)
- Jason Swails (Wed Aug 01 2012 - 06:10:20 PDT)
- Prabu Manoharan (Wed Aug 01 2012 - 06:01:02 PDT)
[AMBER] Problem regarding imin = 5
- Sanjib Paul (Tue Aug 28 2012 - 10:56:54 PDT)
- Sanjib Paul (Tue Aug 28 2012 - 10:54:09 PDT)
- Carlos Simmerling (Tue Aug 28 2012 - 10:53:35 PDT)
- Sanjib Paul (Tue Aug 28 2012 - 10:50:09 PDT)
[AMBER] problem to perform nmode analysis
- Sanjib Paul (Wed Aug 29 2012 - 08:39:33 PDT)
- Jason Swails (Wed Aug 29 2012 - 08:28:18 PDT)
- David A Case (Wed Aug 29 2012 - 08:03:32 PDT)
- Sanjib Paul (Wed Aug 29 2012 - 05:57:21 PDT)
- Sanjib Paul (Wed Aug 29 2012 - 05:41:06 PDT)
[AMBER] problem w/ radial results
- Thomas Cheatham III (Wed Aug 22 2012 - 14:56:37 PDT)
- E. Nihal Korkmaz (Wed Aug 22 2012 - 14:23:04 PDT)
[AMBER] Problem while using acdoctor command
- David A Case (Tue Aug 14 2012 - 05:30:01 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Aug 09 2012 - 23:09:15 PDT)
[AMBER] Problems parameterizing water/ZN active site with MKT++
- Ben Roberts (Tue Aug 14 2012 - 14:27:23 PDT)
- Fabrício Bracht (Tue Aug 14 2012 - 10:55:43 PDT)
- Ben Roberts (Mon Aug 13 2012 - 01:19:10 PDT)
- Ben Roberts (Sun Aug 12 2012 - 02:48:08 PDT)
- Fabrício Bracht (Fri Aug 10 2012 - 05:47:02 PDT)
- Ben Roberts (Sun Aug 05 2012 - 17:43:37 PDT)
- Fabrício Bracht (Sun Aug 05 2012 - 07:39:03 PDT)
- Ben Roberts (Sat Aug 04 2012 - 22:19:53 PDT)
[AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames
- Marek Maly (Fri Aug 17 2012 - 06:59:57 PDT)
- Daniel Roe (Fri Aug 17 2012 - 06:58:21 PDT)
- Marek Maly (Wed Aug 15 2012 - 13:33:39 PDT)
- Daniel Roe (Wed Aug 15 2012 - 13:29:34 PDT)
- Daniel Roe (Wed Aug 15 2012 - 12:55:50 PDT)
- Marek Maly (Wed Aug 15 2012 - 11:21:08 PDT)
- Daniel Roe (Wed Aug 15 2012 - 10:49:18 PDT)
- Marek Maly (Wed Aug 15 2012 - 03:11:31 PDT)
- Daniel Roe (Tue Aug 14 2012 - 15:30:33 PDT)
- Marek Maly (Tue Aug 14 2012 - 11:57:52 PDT)
[AMBER] Production md
- David A Case (Thu Aug 16 2012 - 05:08:34 PDT)
- ariana karakutuk (Thu Aug 16 2012 - 00:55:01 PDT)
- David A Case (Tue Aug 14 2012 - 05:09:23 PDT)
- ariana karakutuk (Tue Aug 14 2012 - 00:19:56 PDT)
- case (Mon Aug 13 2012 - 05:35:01 PDT)
- ariana karakutuk (Mon Aug 13 2012 - 03:06:04 PDT)
[AMBER] protein+DNA simulation
- Dean Cuebas (Thu Aug 23 2012 - 09:50:45 PDT)
- Thomas Cheatham III (Wed Aug 22 2012 - 15:17:41 PDT)
- najmul arfin (Wed Aug 22 2012 - 11:40:18 PDT)
[AMBER] ptraj: msd with diffusion command
- Bala subramanian (Fri Aug 31 2012 - 10:47:14 PDT)
- Dmitry Mukha (Sat Aug 25 2012 - 08:59:06 PDT)
- Daniel Roe (Thu Aug 23 2012 - 12:09:58 PDT)
- Bala subramanian (Thu Aug 23 2012 - 07:41:45 PDT)
[AMBER] Query about how to run ambertools12 after installing it
- David A Case (Tue Aug 14 2012 - 06:40:44 PDT)
- Yousef Elsyid (Tue Aug 14 2012 - 05:04:38 PDT)
[AMBER] question about calculation of PMF with WHAM
- Daniel Sindhikara (Thu Aug 09 2012 - 18:40:00 PDT)
- Yan Li (Wed Aug 08 2012 - 18:43:02 PDT)
- Brian Radak (Wed Aug 08 2012 - 13:11:19 PDT)
- Yan Li (Wed Aug 08 2012 - 10:07:37 PDT)
[AMBER] RECALL More RMS fit
- George Tzotzos (Thu Aug 23 2012 - 05:34:47 PDT)
[AMBER] receptor nmode calculation using amber12 mmpbsa.pl
- Jason Swails (Wed Aug 01 2012 - 10:52:32 PDT)
- manikanthan bhavaraju (Wed Aug 01 2012 - 10:36:55 PDT)
[AMBER] Recommendations for Amber on AMD Bulldozer
- Jan-Philip Gehrcke (Tue Aug 21 2012 - 10:17:42 PDT)
- Ross Walker (Tue Aug 21 2012 - 07:56:49 PDT)
- Jan-Philip Gehrcke (Tue Aug 21 2012 - 05:02:52 PDT)
[AMBER] Reflective Boundary Conditions
- Dr. Vitaly V. G. Chaban (Sun Aug 05 2012 - 13:16:27 PDT)
- case (Sun Aug 05 2012 - 07:13:30 PDT)
- Adam Jion (Fri Aug 03 2012 - 21:17:50 PDT)
[AMBER] resp charge calculation
- FyD (Thu Aug 09 2012 - 09:45:31 PDT)
- jit mukherjee (Wed Aug 08 2012 - 17:44:13 PDT)
[AMBER] RESP charge derivation
- shomesankar bhunia (Thu Aug 30 2012 - 23:13:53 PDT)
- FyD (Thu Aug 30 2012 - 23:06:10 PDT)
- shomesankar bhunia (Thu Aug 30 2012 - 22:51:40 PDT)
- shomesankar bhunia (Thu Aug 30 2012 - 21:02:45 PDT)
- Jason Swails (Thu Aug 30 2012 - 12:21:56 PDT)
- shomesankar bhunia (Thu Aug 30 2012 - 12:04:44 PDT)
- Jason Swails (Thu Aug 30 2012 - 11:55:57 PDT)
- shomesankar bhunia (Thu Aug 30 2012 - 11:49:34 PDT)
[AMBER] Restarting PMEMD calculation after server shutdown
- Jason Swails (Thu Aug 02 2012 - 05:17:38 PDT)
- David A Case (Thu Aug 02 2012 - 05:05:01 PDT)
- Saaz Sakrikar (Thu Aug 02 2012 - 04:07:15 PDT)
[AMBER] Restraint problem
- Fernando Martín García (Fri Aug 10 2012 - 02:59:43 PDT)
- case (Wed Aug 08 2012 - 06:30:05 PDT)
- Fernando Martín García (Wed Aug 08 2012 - 05:27:38 PDT)
- Jason Swails (Wed Aug 08 2012 - 05:09:53 PDT)
- Anselm Horn (Wed Aug 08 2012 - 04:27:22 PDT)
- Fernando Martín García (Wed Aug 08 2012 - 03:35:03 PDT)
- Jérôme Golebiowski (Wed Aug 08 2012 - 03:13:51 PDT)
- Fernando Martín García (Wed Aug 08 2012 - 02:53:15 PDT)
[AMBER] RMS fit
- Daniel Roe (Tue Aug 14 2012 - 10:35:30 PDT)
- Jason Swails (Tue Aug 14 2012 - 10:29:29 PDT)
- Eliac Brown (Tue Aug 14 2012 - 10:06:03 PDT)
- Daniel Roe (Tue Aug 14 2012 - 08:04:10 PDT)
- Eliac Brown (Tue Aug 14 2012 - 07:45:13 PDT)
[AMBER] Segmentation Fault in Tleap
- Jason Swails (Thu Aug 30 2012 - 16:52:28 PDT)
- Deepak Ojha (Thu Aug 30 2012 - 14:19:37 PDT)
[AMBER] specific atom restraint
- Thanh Binh NGUYEN (Fri Aug 10 2012 - 20:08:55 PDT)
- Jason Swails (Fri Aug 10 2012 - 10:04:38 PDT)
- Thanh Binh NGUYEN (Fri Aug 10 2012 - 09:09:47 PDT)
[AMBER] Starting and ending temperatures for REMD
- Sajeewa Pemasinghe (Wed Aug 08 2012 - 10:26:56 PDT)
[AMBER] Switch-off PBC in md-GPU
- David A Case (Fri Aug 03 2012 - 05:17:07 PDT)
- Adam Jion (Fri Aug 03 2012 - 03:42:18 PDT)
[AMBER] Temperature regulation in HREMD
- dani sd (Wed Aug 15 2012 - 13:29:58 PDT)
- Carlos Simmerling (Wed Aug 15 2012 - 12:58:45 PDT)
- dani sd (Wed Aug 15 2012 - 11:39:59 PDT)
- Brian Radak (Wed Aug 15 2012 - 06:39:31 PDT)
[AMBER] Test message please ignore
- Ross Walker (Tue Aug 07 2012 - 22:21:36 PDT)
[AMBER] TI run energy does not conserve
- Brian Radak (Sun Aug 12 2012 - 12:14:34 PDT)
- psu4.uic.edu (Fri Aug 10 2012 - 13:41:22 PDT)
- Brian Radak (Fri Aug 10 2012 - 06:20:51 PDT)
- psu4.uic.edu (Fri Aug 10 2012 - 00:16:10 PDT)
- Brian Radak (Thu Aug 09 2012 - 07:30:48 PDT)
- Pin-Chih Su (Henry Su) (Wed Aug 08 2012 - 15:02:55 PDT)
- Brian Radak (Tue Aug 07 2012 - 07:09:53 PDT)
- Pin-Chih Su (Henry Su) (Mon Aug 06 2012 - 15:51:54 PDT)
- Brian Radak (Fri Aug 03 2012 - 11:44:40 PDT)
- Pin-Chih Su (Henry Su) (Fri Aug 03 2012 - 10:44:03 PDT)
[AMBER] TI with softcore at lambda=0 or 1?
- Liu Denis (Tue Aug 14 2012 - 18:29:16 PDT)
- David A Case (Tue Aug 14 2012 - 05:22:53 PDT)
- Liu Denis (Sun Aug 12 2012 - 08:01:33 PDT)
- case (Sun Aug 12 2012 - 05:55:20 PDT)
- Liu Denis (Sat Aug 11 2012 - 09:37:36 PDT)
- steinbrt.rci.rutgers.edu (Thu Aug 09 2012 - 08:08:40 PDT)
- Liu Denis (Thu Aug 09 2012 - 06:37:15 PDT)
- steinbrt.rci.rutgers.edu (Thu Aug 09 2012 - 01:05:12 PDT)
- Liu Denis (Wed Aug 08 2012 - 10:01:14 PDT)
[AMBER] TMD setup
- Simon Becker (Mon Aug 06 2012 - 02:15:29 PDT)
- Manish Datt (Mon Aug 06 2012 - 01:46:14 PDT)
[AMBER] to draw vector along the axis
- Sangita Kachhap (Fri Aug 03 2012 - 10:54:53 PDT)
[AMBER] transition metal system works on pmemd crashes on pmemd.cuda
- Jason Swails (Wed Aug 22 2012 - 07:50:05 PDT)
- Patrick von Glehn (Wed Aug 22 2012 - 07:28:50 PDT)
- Scott Le Grand (Mon Aug 20 2012 - 19:35:09 PDT)
- Patrick von Glehn (Mon Aug 20 2012 - 16:37:41 PDT)
[AMBER] unique atom names
- case (Fri Aug 10 2012 - 17:54:37 PDT)
- Chris Chris (Fri Aug 10 2012 - 08:56:49 PDT)
[AMBER] where is the subroutine amflsh in Amber10?
- case (Sun Aug 19 2012 - 06:08:00 PDT)
- Xin Geng (Sat Aug 18 2012 - 15:50:38 PDT)
[AMBER] which part of source code implementing GB/SA simulations?
- Xin Geng (Tue Aug 14 2012 - 20:48:24 PDT)
- Xin Geng (Tue Aug 14 2012 - 20:42:10 PDT)
- case (Tue Aug 14 2012 - 19:30:49 PDT)
- Xin Geng (Tue Aug 14 2012 - 16:26:47 PDT)
[AMBER] Zn atom flying off
- moitrayee.mbu.iisc.ernet.in (Fri Aug 17 2012 - 06:55:18 PDT)
frcmod and lib files fro Cadmium
- Mahendra B Thapa (Thu Aug 02 2012 - 14:07:11 PDT)
How to Calculate SASA with Amber?
- Daniel Roe (Sun Aug 19 2012 - 21:20:56 PDT)
- Jason Swails (Sun Aug 19 2012 - 20:59:38 PDT)
- Ross Walker (Sun Aug 19 2012 - 20:58:49 PDT)
- E. Nihal Korkmaz (Sun Aug 19 2012 - 20:52:24 PDT)
- E. Nihal Korkmaz (Sun Aug 19 2012 - 20:49:25 PDT)
problem in converting rst-file to pdb using cpptraj
- Mahendra B Thapa (Wed Aug 01 2012 - 14:18:58 PDT)

Amber Archive Aug 2012 by subject