Amber Archive Dec 2013: by subject

[AMBER] 3D projection of pairwise-RMSD
- David A Case (Fri Dec 13 2013 - 10:08:40 PST)
- Sangeetha B (Fri Dec 13 2013 - 10:00:18 PST)
- Adrian Roitberg (Fri Dec 13 2013 - 09:42:50 PST)
- Adrian Roitberg (Fri Dec 13 2013 - 09:42:42 PST)
- Sangeetha B (Fri Dec 13 2013 - 09:28:52 PST)
- Daniel Roe (Fri Dec 13 2013 - 08:41:05 PST)
- Sangeetha B (Fri Dec 13 2013 - 06:11:57 PST)
[AMBER] accelerated Molecular dynamics
- Jason Swails (Mon Dec 09 2013 - 04:12:03 PST)
- Ibrahim Said (Mon Dec 09 2013 - 00:17:33 PST)
[AMBER] AMBER
- Daniel Roe (Tue Dec 31 2013 - 07:58:39 PST)
- Asfa Ali (Mon Dec 30 2013 - 13:43:52 PST)
- Asfa Ali (Wed Dec 25 2013 - 04:03:41 PST)
[AMBER] AMBER GPU performance issue
- Jason Swails (Tue Dec 10 2013 - 12:42:53 PST)
- Neha Gandhi (Tue Dec 10 2013 - 03:04:37 PST)
[AMBER] amber parameter for S2P (phosphoserine)
- Jonathan Sheehan (Tue Dec 24 2013 - 11:20:35 PST)
- sunita.tifrh.res.in (Tue Dec 24 2013 - 00:32:15 PST)
- sunita.tifrh.res.in (Mon Dec 23 2013 - 22:47:54 PST)
[AMBER] Amber QM/MM
- Ross Walker (Thu Dec 12 2013 - 07:38:32 PST)
- Gustavo Seabra (Wed Dec 11 2013 - 06:57:02 PST)
- Brian Radak (Wed Dec 11 2013 - 06:55:31 PST)
- Fengxue Li (Wed Dec 11 2013 - 05:54:27 PST)
[AMBER] amber QM/MM :vlimit exceeded for step 1; vmax = 71.9072
- Ross Walker (Mon Dec 16 2013 - 09:26:23 PST)
- Brian Radak (Mon Dec 16 2013 - 06:18:13 PST)
- Fengxue Li (Mon Dec 16 2013 - 06:06:30 PST)
[AMBER] Amber Tools v.13
- Jason Swails (Wed Dec 11 2013 - 17:15:47 PST)
- Daniel Roe (Wed Dec 11 2013 - 14:25:12 PST)
- Silvestre (Wed Dec 11 2013 - 12:57:45 PST)
- Silvestre (Mon Dec 09 2013 - 14:25:48 PST)
- Jason Swails (Mon Dec 09 2013 - 14:00:44 PST)
- Silvestre (Mon Dec 09 2013 - 13:18:48 PST)
[AMBER] AMBER12 test discrepancy
- Guanglei Cui (Tue Dec 03 2013 - 07:55:44 PST)
[AMBER] AmberTools update 22 for CPPTRAJ
- Daniel Roe (Fri Dec 13 2013 - 09:04:37 PST)
[AMBER] AMD simulation
- Mele N. (Wed Dec 18 2013 - 03:57:07 PST)
- Mele N. (Wed Dec 18 2013 - 03:47:00 PST)
[AMBER] AMDTutorial
- Ibrahim Said (Fri Dec 27 2013 - 10:08:38 PST)
[AMBER] angle restraint with atom groups
- Sourav Purohit (Mon Dec 30 2013 - 13:30:54 PST)
- David A Case (Mon Dec 30 2013 - 10:58:39 PST)
- Sourav Purohit (Mon Dec 30 2013 - 10:49:08 PST)
[AMBER] Anisotropic & semi-anisotropic
- Vijay Manickam Achari (Mon Dec 09 2013 - 19:35:11 PST)
- Jason Swails (Sat Dec 07 2013 - 07:32:09 PST)
- Vijay Manickam Achari (Sat Dec 07 2013 - 00:46:54 PST)
[AMBER] anisotropic & semi-anisotropic pressure coupling.
- Vijay Manickam Achari (Fri Dec 06 2013 - 01:24:29 PST)
[AMBER] ANTECHAMBER PROBLEM
- David A Case (Fri Dec 20 2013 - 10:41:17 PST)
- Arjun Sharma (Fri Dec 20 2013 - 08:50:08 PST)
[AMBER] Atom Expression in NAB
- Jason Swails (Mon Dec 09 2013 - 04:08:20 PST)
- sunita gupta (Sun Dec 08 2013 - 21:21:09 PST)
- sunita gupta (Sun Dec 08 2013 - 21:11:49 PST)
- case (Sun Dec 08 2013 - 08:29:57 PST)
- sunita gupta (Sun Dec 08 2013 - 07:59:58 PST)
[AMBER] atom-atom contact analysis in PTRAj
- Pranjal Mahanta (Wed Dec 11 2013 - 23:51:09 PST)
[AMBER] Bad atom type error during MMGBSA decomposition calsulations
- Jason Swails (Thu Dec 19 2013 - 07:47:36 PST)
- 王衍 (Thu Dec 19 2013 - 00:47:06 PST)
[AMBER] binding free energy and pose analysis
- Nitin Sharma (Sun Dec 29 2013 - 09:23:58 PST)
- Jason Swails (Sun Dec 29 2013 - 09:10:31 PST)
- Nitin Sharma (Sun Dec 29 2013 - 07:44:24 PST)
- case (Sat Dec 28 2013 - 05:38:04 PST)
- Nitin Sharma (Sat Dec 28 2013 - 02:42:59 PST)
- case (Fri Dec 27 2013 - 18:58:49 PST)
- Nitin Sharma (Fri Dec 27 2013 - 09:52:50 PST)
[AMBER] Brookhaven pdb format
- 闫玉娜 (Sun Dec 08 2013 - 21:04:44 PST)
- Daniel Roe (Sun Dec 08 2013 - 19:53:07 PST)
- 闫玉娜 (Sun Dec 08 2013 - 19:22:40 PST)
[AMBER] C12 from OL
- Rejwan (Tue Dec 31 2013 - 10:32:08 PST)
[AMBER] Calculation of NMR relaxation rates
- Daniel Roe (Wed Dec 04 2013 - 08:17:00 PST)
- case (Tue Dec 03 2013 - 18:39:33 PST)
- Mahendra B Thapa (Mon Dec 02 2013 - 16:43:10 PST)
[AMBER] capturing free energy landscape
- Daniel Roe (Tue Dec 31 2013 - 08:04:46 PST)
- anu chandra (Mon Dec 30 2013 - 03:04:13 PST)
- Daniel Roe (Thu Dec 26 2013 - 06:35:45 PST)
- anu chandra (Thu Dec 26 2013 - 03:59:03 PST)
- Thomas Evangelidis (Fri Dec 20 2013 - 05:35:31 PST)
- Jason Swails (Fri Dec 20 2013 - 04:03:37 PST)
- anu chandra (Fri Dec 20 2013 - 00:55:50 PST)
- anu chandra (Wed Dec 11 2013 - 03:09:46 PST)
- Adrian Roitberg (Tue Dec 10 2013 - 13:26:58 PST)
- Thomas Evangelidis (Tue Dec 10 2013 - 12:59:46 PST)
- Jason Swails (Tue Dec 10 2013 - 12:45:46 PST)
- anu chandra (Tue Dec 10 2013 - 02:23:46 PST)
[AMBER] changeLJSingleType problem in parmed.py
- Jason Swails (Thu Dec 12 2013 - 14:45:30 PST)
- Hamed S. Hayatshahi (Thu Dec 12 2013 - 14:26:29 PST)
[AMBER] Compare the result between pmemd.cuda and pmemd.mpi?
- Jason Swails (Mon Dec 02 2013 - 10:49:42 PST)
- Ross Walker (Mon Dec 02 2013 - 10:42:49 PST)
- X Sun (Mon Dec 02 2013 - 10:11:42 PST)
[AMBER] compile parallel mpi
- Jason Swails (Fri Dec 06 2013 - 08:50:40 PST)
- Zahra Khatti (Fri Dec 06 2013 - 06:55:03 PST)
[AMBER] constant pH
- David A Case (Thu Dec 05 2013 - 05:01:03 PST)
- Kshatresh Dutta Dubey (Thu Dec 05 2013 - 04:53:03 PST)
- anurag.dobhal (Thu Dec 05 2013 - 04:36:08 PST)
- anurag.dobhal (Thu Dec 05 2013 - 04:32:04 PST)
[AMBER] Converting Amoeba .xyz for use with Amber
- Eugene Yedvabny (Sat Dec 14 2013 - 16:01:27 PST)
- case (Sat Dec 14 2013 - 08:09:50 PST)
- Eugene Yedvabny (Fri Dec 13 2013 - 14:08:40 PST)
- Eugene Yedvabny (Mon Dec 09 2013 - 14:27:38 PST)
- Eugene Yedvabny (Mon Dec 09 2013 - 14:24:31 PST)
- Jason Swails (Fri Dec 06 2013 - 14:11:08 PST)
- David A Case (Fri Dec 06 2013 - 05:27:10 PST)
- Eugene Yedvabny (Thu Dec 05 2013 - 20:05:09 PST)
[AMBER] cpptraj can not pass empty trajectory entry which is ok for ptraj
- Asaminew Haile (Fri Dec 20 2013 - 09:43:07 PST)
- Daniel Roe (Fri Dec 20 2013 - 09:39:51 PST)
- ros (Fri Dec 20 2013 - 09:00:37 PST)
- Asaminew Haile (Fri Dec 20 2013 - 08:52:56 PST)
[AMBER] cpptraj clustering
- Daniel Roe (Thu Dec 26 2013 - 06:44:17 PST)
- Neha Gandhi (Thu Dec 26 2013 - 03:03:39 PST)
[AMBER] cpptraj output and hbond
- André C. Stiel (Wed Dec 11 2013 - 11:10:55 PST)
- André C. Stiel (Wed Dec 11 2013 - 01:40:12 PST)
[AMBER] CpptrajPairDist
- JAIME RUBIO MARTINEZ (Sat Dec 28 2013 - 11:58:49 PST)
- Daniel Roe (Tue Dec 17 2013 - 13:52:15 PST)
- Daniel Roe (Tue Dec 17 2013 - 13:44:32 PST)
- JAIME RUBIO MARTINEZ (Tue Dec 17 2013 - 11:37:28 PST)
[AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
- Ross Walker (Sat Dec 21 2013 - 11:23:20 PST)
- filip fratev (Sat Dec 21 2013 - 11:08:39 PST)
[AMBER] Does anyone know which parameter controls the wavenumber related to the Helmholtz equation
- wmsmith.uci.edu (Tue Dec 10 2013 - 10:08:12 PST)
- 肖立 (Tue Dec 10 2013 - 09:03:15 PST)
- wmsmith.uci.edu (Tue Dec 10 2013 - 08:11:45 PST)
- 肖立 (Mon Dec 09 2013 - 20:47:04 PST)
[AMBER] Does anyone knows how to generate an ired vector
- 肖立 (Wed Dec 11 2013 - 21:36:37 PST)
- Daniel Roe (Wed Dec 11 2013 - 20:07:42 PST)
- Daniel Roe (Wed Dec 11 2013 - 19:57:49 PST)
- wmsmith.uci.edu (Wed Dec 11 2013 - 16:45:28 PST)
- 肖立 (Wed Dec 11 2013 - 15:49:47 PST)
- Daniel Roe (Wed Dec 11 2013 - 15:10:24 PST)
- 肖立 (Wed Dec 11 2013 - 14:51:47 PST)
[AMBER] Does pmemd or pmemd.mpi support center of mass restraint?
- Ross Walker (Fri Dec 13 2013 - 12:25:18 PST)
- Igor Marques (Fri Dec 13 2013 - 12:17:57 PST)
- zhongqiao hu (Sun Dec 01 2013 - 06:52:35 PST)
- zhongqiao hu (Sat Nov 30 2013 - 08:01:36 PST)
[AMBER] doubt in alanine scanning of phosphorylated residue
- Jason Swails (Tue Dec 24 2013 - 10:57:55 PST)
- Jason Swails (Mon Dec 23 2013 - 05:44:55 PST)
- suma jayakrishnan (Mon Dec 23 2013 - 02:39:08 PST)
[AMBER] Error in amber12 serial installation in file alltasks_setup.F90:352
- Jason Swails (Fri Dec 06 2013 - 14:04:58 PST)
- David A Case (Fri Dec 06 2013 - 05:14:14 PST)
- Sajeewa Pemasinghe (Thu Dec 05 2013 - 19:46:38 PST)
[AMBER] error in installing ambertools 1.2
- case (Sat Dec 14 2013 - 08:18:33 PST)
- anurag.dobhal (Fri Dec 13 2013 - 10:31:31 PST)
[AMBER] Error while visualizing radius of gyration graph
- Jonathan Sheehan (Wed Dec 18 2013 - 07:15:35 PST)
- David A Case (Wed Dec 18 2013 - 04:58:21 PST)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Tue Dec 17 2013 - 22:56:03 PST)
[AMBER] Errors about the values of PBSUR when calculating binding energy using MMPBSA
- Jason Swails (Wed Dec 25 2013 - 06:55:08 PST)
- Yanyan ZHU (Wed Dec 25 2013 - 01:35:57 PST)
[AMBER] ErrorWithLeap
- Jason Swails (Tue Dec 24 2013 - 10:18:39 PST)
- JAIME RUBIO MARTINEZ (Tue Dec 24 2013 - 09:14:55 PST)
- Jason Swails (Mon Dec 23 2013 - 19:29:43 PST)
- case (Mon Dec 23 2013 - 19:24:48 PST)
- case (Mon Dec 23 2013 - 19:21:16 PST)
- JAIME RUBIO MARTINEZ (Mon Dec 23 2013 - 16:17:20 PST)
[AMBER] FINAL_RESULTS_MMPBSA error
- Jason Swails (Fri Dec 20 2013 - 03:58:03 PST)
- filip fratev (Thu Dec 19 2013 - 23:23:41 PST)
[AMBER] Finding difficulty during calculation of diffusion coefficient from MSD plot
- Sohag Biswas (Sat Dec 28 2013 - 21:40:33 PST)
[AMBER] Fwd:
- Asfa Ali (Mon Dec 30 2013 - 13:44:13 PST)
- Jason Swails (Sat Dec 28 2013 - 10:17:37 PST)
- Asfa Ali (Sat Dec 28 2013 - 01:40:31 PST)
- Jason Swails (Thu Dec 26 2013 - 18:33:01 PST)
- Asfa Ali (Thu Dec 26 2013 - 05:37:55 PST)
- Jason Swails (Wed Dec 25 2013 - 11:42:52 PST)
- Asfa Ali (Wed Dec 25 2013 - 04:01:04 PST)
[AMBER] Fwd: doubt in alanine scanning of phosphorylated residue
- suma jayakrishnan (Tue Dec 24 2013 - 18:45:17 PST)
[AMBER] Help: Producing a Prmtop file for a Truncated-Protein Trajectory
- Jason Swails (Mon Dec 16 2013 - 05:11:05 PST)
- #YIP YEW MUN# (Sun Dec 15 2013 - 21:22:37 PST)
[AMBER] How to compile amber12 in AIX UNIX?
- Mengyuan Zhu (Thu Dec 05 2013 - 21:17:46 PST)
- Daniel Roe (Tue Dec 03 2013 - 20:26:50 PST)
- Mengyuan Zhu (Tue Dec 03 2013 - 19:05:40 PST)
- Mengyuan Zhu (Tue Dec 03 2013 - 18:55:37 PST)
- case (Tue Dec 03 2013 - 18:22:31 PST)
- Mengyuan Zhu (Tue Dec 03 2013 - 11:19:32 PST)
[AMBER] How to decompose PMF into electrostatic and van der Waals contributions
- Jason Swails (Thu Dec 26 2013 - 13:48:16 PST)
- zhongqiao hu (Thu Dec 26 2013 - 06:10:34 PST)
- Brian Radak (Tue Dec 24 2013 - 14:34:12 PST)
- zhongqiao hu (Sat Dec 21 2013 - 05:48:42 PST)
- David A Case (Fri Dec 20 2013 - 06:37:41 PST)
- zhongqiao hu (Thu Dec 19 2013 - 18:35:41 PST)
[AMBER] How to decompose PMF into electrostatic and van der Waals contributions.
- Brian Radak (Thu Dec 19 2013 - 06:39:58 PST)
- zhongqiao hu (Thu Dec 19 2013 - 01:44:00 PST)
[AMBER] how to minimize with full electrostatics and no boundary conditions?
- Jose Borreguero (Tue Dec 31 2013 - 11:26:06 PST)
- David A Case (Tue Dec 31 2013 - 05:14:24 PST)
- Jose Borreguero (Mon Dec 30 2013 - 12:59:33 PST)
- Jason Swails (Mon Dec 30 2013 - 12:32:21 PST)
- Jose Borreguero (Mon Dec 30 2013 - 11:36:15 PST)
[AMBER] how to remove the rotational center-of-mass motion ?
- David A Case (Fri Dec 13 2013 - 04:44:41 PST)
- 张明焜 (Thu Dec 12 2013 - 22:30:26 PST)
[AMBER] I got a error
- Jason Swails (Fri Dec 13 2013 - 09:10:14 PST)
- David Chen (Fri Dec 13 2013 - 02:42:35 PST)
- David Chen (Thu Dec 12 2013 - 04:22:58 PST)
[AMBER] Improper terms in Amber
- case (Mon Dec 16 2013 - 17:48:30 PST)
- Meng (Mon Dec 16 2013 - 13:26:11 PST)
[AMBER] input file with leap or antechamber?
- Ye MEI (Wed Dec 25 2013 - 00:18:01 PST)
- Zahra Khatti (Wed Dec 25 2013 - 00:02:19 PST)
[AMBER] internal geometry restraint
- David A Case (Mon Dec 02 2013 - 12:06:53 PST)
- Jio M (Mon Dec 02 2013 - 09:50:42 PST)
- David A Case (Mon Dec 02 2013 - 05:04:10 PST)
- Jio M (Sun Dec 01 2013 - 16:41:12 PST)
[AMBER] Is restart file size different between minimization and heating MD?
- Biao Ma (Thu Dec 19 2013 - 08:36:22 PST)
- David A Case (Wed Dec 18 2013 - 04:57:01 PST)
- Biao Ma (Tue Dec 17 2013 - 22:08:13 PST)
[AMBER] Is there any way I can complete a production run which has been interrupted by a sudden power cut ?
- Roza M (Wed Dec 11 2013 - 08:29:42 PST)
- Gustavo Seabra (Wed Dec 11 2013 - 06:58:16 PST)
- Roza M (Wed Dec 11 2013 - 05:44:14 PST)
[AMBER] issues with MMPBSA tutorial/MMPBSA.py
- Bennion, Brian (Fri Dec 13 2013 - 11:03:42 PST)
[AMBER] Keeping an hexamer whole.
- Julio Dominguez (Thu Dec 05 2013 - 21:06:33 PST)
- Daniel Roe (Wed Dec 04 2013 - 20:27:42 PST)
- Jason Swails (Wed Dec 04 2013 - 17:56:13 PST)
- Julio Dominguez (Wed Dec 04 2013 - 16:38:16 PST)
[AMBER] Manually extending the size of the virtual box
- case (Thu Dec 26 2013 - 07:08:41 PST)
- Eugene Yedvabny (Mon Dec 16 2013 - 17:58:33 PST)
- Jason Swails (Mon Dec 16 2013 - 12:12:54 PST)
- Carlos Simmerling (Mon Dec 16 2013 - 11:18:42 PST)
- Eugene Yedvabny (Mon Dec 16 2013 - 11:03:54 PST)
- David A Case (Mon Dec 16 2013 - 04:30:00 PST)
- Eugene Yedvabny (Mon Dec 16 2013 - 01:19:44 PST)
[AMBER] math operations in cpptraj
- Daniel Roe (Mon Dec 09 2013 - 08:43:09 PST)
- Andre C. Stiel (Mon Dec 09 2013 - 08:26:14 PST)
[AMBER] MGMS-DS: Molecular Modelling Workshop 2014 in Erlangen, Germany
- Harald Lanig (Fri Dec 13 2013 - 01:29:25 PST)
[AMBER] MMGBSA Entropy Error: Trajectory _MMPBSA_complex.mdcrd.1 has 0 frames!
- Cuiyl (Tue Dec 17 2013 - 18:13:22 PST)
[AMBER] MMPBSA errors :failed with prmtop
- Ray Luo, Ph.D. (Mon Dec 16 2013 - 15:13:44 PST)
- Ray Luo, Ph.D. (Tue Dec 10 2013 - 10:04:22 PST)
- Fengxue Li (Tue Dec 10 2013 - 01:49:53 PST)
[AMBER] MMPBSA errors ：setting grid spacing larger than solvent probe
- Ray Luo, Ph.D. (Mon Dec 09 2013 - 10:03:18 PST)
- Jason Swails (Mon Dec 09 2013 - 07:53:55 PST)
- Fengxue Li (Mon Dec 09 2013 - 05:25:09 PST)
[AMBER] MMPBSA for single re-minimised coordinate
- Jason Swails (Mon Dec 23 2013 - 05:50:47 PST)
- sunita gupta (Mon Dec 23 2013 - 04:23:31 PST)
[AMBER] MMPBSA of protein_DNA complex
- Vlad Cojocaru (Tue Dec 17 2013 - 02:49:06 PST)
- Aditya sarkar (Tue Dec 17 2013 - 02:18:21 PST)
[AMBER] MMPBSA with inp=1
- Ray Luo, Ph.D. (Mon Dec 23 2013 - 11:31:30 PST)
- wmsmith.uci.edu (Thu Dec 19 2013 - 11:49:41 PST)
- wmsmith.uci.edu (Thu Dec 19 2013 - 11:47:06 PST)
- Ray Luo, Ph.D. (Thu Dec 19 2013 - 10:34:21 PST)
- Vlad Cojocaru (Thu Dec 19 2013 - 10:28:07 PST)
- Ray Luo, Ph.D. (Thu Dec 19 2013 - 09:40:05 PST)
- Vlad Cojocaru (Thu Dec 19 2013 - 02:38:25 PST)
[AMBER] MMPBSA.py strip_mask issue
- Jason Swails (Mon Dec 16 2013 - 05:29:37 PST)
- psu4.uic.edu (Sun Dec 15 2013 - 20:52:43 PST)
[AMBER] MMPBSA: eneopt=1 versus eneopt=3
- Vlad Cojocaru (Mon Dec 16 2013 - 08:06:51 PST)
[AMBER] modified the amber parameter
- Jason Swails (Wed Dec 25 2013 - 12:10:24 PST)
- Saeed Nasiri (Wed Dec 25 2013 - 08:12:13 PST)
[AMBER] nasiri
- Jason Swails (Wed Dec 04 2013 - 07:15:04 PST)
- Saeed Nasiri (Wed Dec 04 2013 - 07:00:02 PST)
[AMBER] Need some advice on calculating diffusion constant
- Brian Radak (Mon Dec 16 2013 - 06:05:15 PST)
[AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c
- Daniel Roe (Tue Dec 10 2013 - 10:18:42 PST)
- Sajeewa Pemasinghe (Tue Dec 10 2013 - 10:14:24 PST)
- Jason Swails (Mon Dec 09 2013 - 17:40:59 PST)
- Aldo Segura (Mon Dec 09 2013 - 17:13:18 PST)
- Sajeewa Pemasinghe (Mon Dec 09 2013 - 16:25:59 PST)
[AMBER] not getting correct density for N,N-dimethylformamide
- David A Case (Mon Dec 09 2013 - 13:16:33 PST)
- FyD (Sat Dec 07 2013 - 13:12:23 PST)
- Sohag Biswas (Sat Dec 07 2013 - 08:39:58 PST)
[AMBER] parmed.py setBond
- Jason Swails (Tue Dec 03 2013 - 14:51:20 PST)
- Aronica, Pietro (Tue Dec 03 2013 - 11:43:17 PST)
- Jason Swails (Tue Dec 03 2013 - 11:22:48 PST)
- Jason Swails (Tue Dec 03 2013 - 11:04:36 PST)
- Jason Swails (Tue Dec 03 2013 - 10:45:49 PST)
- Aronica, Pietro (Tue Dec 03 2013 - 10:25:21 PST)
- Brian Radak (Tue Dec 03 2013 - 10:07:30 PST)
- Aronica, Pietro (Tue Dec 03 2013 - 10:03:14 PST)
- Brian Radak (Tue Dec 03 2013 - 09:59:47 PST)
- Aronica, Pietro (Tue Dec 03 2013 - 09:44:27 PST)
[AMBER] PARSE radii and effective radii IN MM/PBSA & MM/GBSA
- Ray Luo, Ph.D. (Mon Dec 02 2013 - 16:35:17 PST)
- psu4.uic.edu (Mon Dec 02 2013 - 15:52:40 PST)
[AMBER] pbsa: solvation radius from topology file not used when radiopt=0
- wmsmith.uci.edu (Tue Dec 03 2013 - 12:21:15 PST)
- Ray Luo, Ph.D. (Tue Dec 03 2013 - 10:38:47 PST)
- Jan-Philip Gehrcke (Tue Dec 03 2013 - 04:54:29 PST)
[AMBER] planarity of Trp side chain and improper torsion term
- case (Sun Dec 01 2013 - 14:23:28 PST)
- Jorge Iulek (Sun Dec 01 2013 - 03:30:21 PST)
[AMBER] please tell me why this error is coming while doing the constant pH MD
- Jason Swails (Mon Dec 09 2013 - 11:30:09 PST)
- anurag.dobhal (Mon Dec 09 2013 - 10:37:47 PST)
[AMBER] Plotting a Dynamic Cross Correlation Map
- Yip Yew Mun (Fri Dec 06 2013 - 00:28:25 PST)
[AMBER] Plotting heat maps in AMBER aMD simualtions
- Daniel Roe (Wed Dec 11 2013 - 10:38:40 PST)
- filip fratev (Wed Dec 11 2013 - 10:18:20 PST)
- Jason Swails (Wed Dec 11 2013 - 09:52:19 PST)
- Brian Radak (Wed Dec 11 2013 - 08:10:32 PST)
- filip fratev (Wed Dec 11 2013 - 07:56:58 PST)
[AMBER] Polarizing solute in non-polarizing solvent
- case (Thu Dec 26 2013 - 07:00:18 PST)
- Hemant Gangwar (Tue Dec 24 2013 - 12:02:19 PST)
[AMBER] Problem when calculating MMPBSA
- Jason Swails (Thu Dec 26 2013 - 23:03:35 PST)
- dongying0512 (Thu Dec 26 2013 - 22:53:49 PST)
- dongying0512 (Thu Dec 26 2013 - 22:50:34 PST)
[AMBER] Problem when calculating MMPBSA (Jason Swails)
- dongying0512 (Sun Dec 29 2013 - 17:21:37 PST)
[AMBER] Problems about invoking AMBER12 in calculating binding energy
- Jason Swails (Thu Dec 26 2013 - 18:36:45 PST)
- Yanyan ZHU (Thu Dec 26 2013 - 18:19:00 PST)
[AMBER] problems in nmode and -use-mdins option (MMPBSA.py)
- houcemeddine (Tue Dec 24 2013 - 11:09:15 PST)
- Jason Swails (Tue Dec 24 2013 - 10:31:07 PST)
- houcemeddine (Tue Dec 24 2013 - 07:55:12 PST)
[AMBER] Problems of invoking the Amber 12
- Jason Swails (Fri Dec 20 2013 - 04:02:35 PST)
- Yanyan ZHU (Thu Dec 19 2013 - 23:53:41 PST)
[AMBER] Problems of invoking the Amber 12 and calculating the energy of each residue using the MMPBSA
- Yanyan ZHU (Sat Dec 21 2013 - 20:13:29 PST)
[AMBER] Proper Algorithm for GPU?
- case (Sun Dec 15 2013 - 10:06:26 PST)
- X Sun (Sat Dec 14 2013 - 15:31:10 PST)
[AMBER] ptraj hbond output format
- Jan-Philip Gehrcke (Sun Dec 08 2013 - 07:26:40 PST)
- André C. Stiel (Sun Dec 08 2013 - 03:39:54 PST)
- Daniel Roe (Fri Dec 06 2013 - 16:05:38 PST)
- Andre C. Stiel (Fri Dec 06 2013 - 05:39:47 PST)
[AMBER] Puzzles about calculating binding energy using MMGBSA
- Jason Swails (Thu Dec 19 2013 - 14:18:42 PST)
- Jason Swails (Sat Dec 14 2013 - 06:44:07 PST)
- Yanyan ZHU (Sat Dec 14 2013 - 04:05:41 PST)
[AMBER] Puzzles about calculating the binding energy of residues
- Yanyan ZHU (Thu Dec 12 2013 - 06:10:40 PST)
[AMBER] question
- Hamed S. Hayatshahi (Thu Dec 05 2013 - 09:38:43 PST)
- Jason Swails (Thu Dec 05 2013 - 09:35:57 PST)
- Zahra Khatti (Thu Dec 05 2013 - 09:13:37 PST)
[AMBER] Regarding distance between residue masks (ptraj)
- agarai.physics.iisc.ernet.in (Sun Dec 22 2013 - 00:12:04 PST)
- Jason Swails (Thu Dec 19 2013 - 07:45:53 PST)
- Daniel Roe (Thu Dec 19 2013 - 07:37:58 PST)
- agarai.physics.iisc.ernet.in (Thu Dec 19 2013 - 04:47:13 PST)
[AMBER] Regarding generating parameters for protein with NAD+
- case (Wed Dec 11 2013 - 18:19:34 PST)
- Prema Mallipeddi (Wed Dec 11 2013 - 14:49:55 PST)
[AMBER] request for help in water shell and closest command
- Daniel Roe (Tue Dec 31 2013 - 08:27:29 PST)
- Robin Jain (Sun Dec 29 2013 - 22:43:57 PST)
[AMBER] Restrained MD with COM restraint with PMEMD
- Jason Swails (Wed Dec 04 2013 - 04:51:15 PST)
- Mike Limb (Wed Dec 04 2013 - 03:41:03 PST)
- case (Tue Dec 03 2013 - 18:33:17 PST)
- Mike Limb (Tue Dec 03 2013 - 14:16:59 PST)
[AMBER] RE： Bad atom type error during MMGBSA decompositioncalsulations
- wangyanforward.gmail.com (Thu Dec 19 2013 - 18:47:33 PST)
[AMBER] RMSD vs RMSF vs nofit-RMSD
- Daniel Roe (Tue Dec 31 2013 - 08:47:46 PST)
- Nitin Sharma (Fri Dec 27 2013 - 09:29:06 PST)
- Daniel Roe (Fri Dec 27 2013 - 06:01:12 PST)
- vadiraj kurdekar (Fri Dec 27 2013 - 02:34:33 PST)
- Nitin Sharma (Thu Dec 26 2013 - 09:40:05 PST)
[AMBER] RMSD-based clustering in CPPTRAJ/PTRAJ
- Daniel Roe (Fri Dec 20 2013 - 07:39:18 PST)
- anu chandra (Thu Dec 19 2013 - 21:53:36 PST)
[AMBER] RMSF
- Jason Swails (Thu Dec 05 2013 - 07:41:26 PST)
- John Smith (Thu Dec 05 2013 - 07:22:39 PST)
- John Smith (Thu Dec 05 2013 - 07:03:30 PST)
- Jason Swails (Thu Dec 05 2013 - 05:54:39 PST)
- John Smith (Thu Dec 05 2013 - 05:32:12 PST)
- Jason Swails (Thu Dec 05 2013 - 05:04:22 PST)
- David A Case (Thu Dec 05 2013 - 05:02:58 PST)
- John Smith (Thu Dec 05 2013 - 04:41:14 PST)
[AMBER] runing sander
- Jason Swails (Wed Dec 11 2013 - 09:53:27 PST)
- Saeed Nasiri (Wed Dec 11 2013 - 07:38:50 PST)
[AMBER] sander command
- Jason Swails (Wed Dec 11 2013 - 04:22:10 PST)
- Saeed Nasiri (Tue Dec 10 2013 - 00:07:37 PST)
[AMBER] sander's Segmentation fault
- case (Sat Dec 28 2013 - 05:40:58 PST)
- Saeed Nasiri (Sat Dec 28 2013 - 03:36:13 PST)
[AMBER] saveamberparameters problem
- David A Case (Mon Dec 02 2013 - 11:59:56 PST)
- Saeed Nasiri (Mon Dec 02 2013 - 08:25:22 PST)
[AMBER] SETTING QM ZONE
- Tanmoy Paul (Mon Dec 02 2013 - 02:52:46 PST)
[AMBER] Should vdW cutoff distance be system-dependent?
- Brian Radak (Fri Dec 06 2013 - 12:03:53 PST)
- David A Case (Fri Dec 06 2013 - 11:22:27 PST)
- yunshi11 . (Fri Dec 06 2013 - 09:38:28 PST)
[AMBER] Simulating protein with Fe atom
- case (Thu Dec 26 2013 - 06:55:59 PST)
- onetwo (Tue Dec 24 2013 - 20:45:50 PST)
[AMBER] Simulation time help
- Nicole Ippolito (Thu Dec 12 2013 - 08:56:56 PST)
- Adrian Roitberg (Thu Dec 12 2013 - 08:48:20 PST)
- Nicole Ippolito (Thu Dec 12 2013 - 08:44:45 PST)
- Adrian Roitberg (Thu Dec 12 2013 - 08:30:49 PST)
- Nicole Ippolito (Thu Dec 12 2013 - 08:28:31 PST)
[AMBER] SQM seems to run out of memory?
- David A Case (Tue Dec 31 2013 - 05:10:40 PST)
- Jonathan Saboury (Mon Dec 30 2013 - 11:20:37 PST)
[AMBER] status of the Amber lipid framework?
- Ross Walker (Thu Dec 19 2013 - 12:01:21 PST)
- Sally Pias (Thu Dec 19 2013 - 11:54:59 PST)
[AMBER] Temperature raises abnormally during accelerated MD
- O Z (Wed Dec 04 2013 - 17:02:19 PST)
[AMBER] The use of ansiotropic & semi-anisotropic pressure couplings in bilayer simulation.
- Dickson, Callum J (Tue Dec 17 2013 - 09:37:23 PST)
- Vijay Manickam Achari (Wed Dec 11 2013 - 20:20:00 PST)
[AMBER] Tleap Problem - Unable to bond atoms in amide linkages
- David A Case (Mon Dec 30 2013 - 04:41:41 PST)
- Yip Yew Mun (Mon Dec 30 2013 - 01:27:02 PST)
- Mohammed Khaled Tumbi (Mon Dec 30 2013 - 00:54:23 PST)
- #YIP YEW MUN# (Mon Dec 30 2013 - 00:43:15 PST)
[AMBER] Topology files of homodimer-ligand complex
- Jason Swails (Thu Dec 05 2013 - 07:20:20 PST)
[AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file
- case (Fri Dec 27 2013 - 06:09:30 PST)
- onetwo (Thu Dec 26 2013 - 22:42:40 PST)
- case (Thu Dec 26 2013 - 06:48:49 PST)
- onetwo (Wed Dec 25 2013 - 21:57:20 PST)
[AMBER] Using the RED Server Dev. to parameterize a model transition state
- FyD (Mon Dec 16 2013 - 01:49:30 PST)
- Kamali Sripathi (Sun Dec 15 2013 - 15:43:19 PST)
- FyD (Fri Dec 13 2013 - 07:30:51 PST)
- Kamali Sripathi (Fri Dec 13 2013 - 06:56:26 PST)
- FyD (Fri Dec 13 2013 - 01:24:35 PST)
- FyD (Wed Dec 11 2013 - 22:36:42 PST)
- FyD (Wed Dec 11 2013 - 21:21:51 PST)
- Kamali Sripathi (Wed Dec 11 2013 - 12:56:35 PST)
- Kamali Sripathi (Tue Dec 10 2013 - 05:12:58 PST)
- FyD (Mon Dec 09 2013 - 23:52:41 PST)
- Kamali Sripathi (Mon Dec 09 2013 - 15:26:00 PST)
- FyD (Mon Dec 09 2013 - 11:56:21 PST)
- Kamali Sripathi (Mon Dec 09 2013 - 08:30:10 PST)
- FyD (Sat Dec 07 2013 - 13:30:00 PST)
- Kamali Sripathi (Fri Dec 06 2013 - 13:19:46 PST)
[AMBER] When to use semi-anisotropic pressure couplings
- Vijay Manickam Achari (Thu Dec 05 2013 - 22:34:33 PST)
[AMBER] xLeap
- Bill Ross (Fri Dec 27 2013 - 18:20:13 PST)
- Jio M (Fri Dec 27 2013 - 17:45:57 PST)
- case (Fri Dec 27 2013 - 06:23:07 PST)
- Himanshu Joshi (Fri Dec 27 2013 - 04:08:07 PST)
[AMBER] zinc parameters
- Hallel Freedman (Thu Dec 05 2013 - 06:30:56 PST)
- Bill Ross (Wed Dec 04 2013 - 23:46:13 PST)
- Hallel Freedman (Tue Dec 03 2013 - 10:30:47 PST)
- Bill Ross (Tue Dec 03 2013 - 10:26:07 PST)
- Hallel Freedman (Tue Dec 03 2013 - 10:13:43 PST)
- Hallel Freedman (Mon Dec 02 2013 - 16:46:50 PST)
Using the RED Server Dev. to parameterize a model transition state
- FyD (Mon Dec 09 2013 - 12:00:15 PST)

Amber Archive Dec 2013 by subject