Amber Archive Aug 2013: by subject

[AMBER-Developers] GTX-Titan / GTX780 Fix
- Ross Walker (Mon Aug 05 2013 - 17:01:26 PDT)
[AMBER] "All hydrogens" in antechamber
- Barnett, James W. (Mon Aug 26 2013 - 06:42:55 PDT)
- David Case (Sat Aug 24 2013 - 16:17:50 PDT)
- Barnett, James W. (Sat Aug 24 2013 - 08:44:18 PDT)
[AMBER] 10 ns explicit water NPT
- Wang Chern Hoe (Dr) (Fri Aug 02 2013 - 16:24:31 PDT)
- Daniel Roe (Fri Aug 02 2013 - 10:32:30 PDT)
- Wang Chern Hoe (Dr) (Fri Aug 02 2013 - 08:32:47 PDT)
- Daniel Roe (Fri Aug 02 2013 - 08:07:11 PDT)
- Wang Chern Hoe (Dr) (Fri Aug 02 2013 - 07:54:22 PDT)
- David A Case (Fri Aug 02 2013 - 05:26:37 PDT)
- Wang Chern Hoe (Dr) (Fri Aug 02 2013 - 02:22:23 PDT)
[AMBER] 2nd Announcement AMBER workshop in Brazil (Oct 7-11 2013) pre-registration open
- Ross Walker (Wed Aug 21 2013 - 19:46:51 PDT)
- psu4.uic.edu (Wed Aug 21 2013 - 19:38:08 PDT)
- Ross Walker (Sun Aug 11 2013 - 23:01:01 PDT)
- Angelica Parente (Sun Aug 11 2013 - 22:23:27 PDT)
- Ross Walker (Sun Aug 11 2013 - 15:35:49 PDT)
[AMBER] Abnormal md output
- Hailin Huang (Thu Aug 08 2013 - 14:37:59 PDT)
- Ross Walker (Thu Aug 08 2013 - 12:02:59 PDT)
- Hailin Huang (Thu Aug 08 2013 - 11:38:47 PDT)
[AMBER] About SNB range in statistics command in cpptraj
- arundhati dutta (Mon Aug 26 2013 - 09:20:23 PDT)
- Daniel Roe (Mon Aug 26 2013 - 08:51:09 PDT)
- arundhati dutta (Mon Aug 26 2013 - 07:58:22 PDT)
[AMBER] Add potential energy term
- David A Case (Wed Aug 14 2013 - 04:38:04 PDT)
- William Cantara (Tue Aug 13 2013 - 09:24:45 PDT)
[AMBER] AMBER Digest, Vol 587, Issue 1
- Julio Dominguez (Thu Aug 22 2013 - 19:43:17 PDT)
- Karl N. Kirschner (Wed Aug 21 2013 - 00:49:49 PDT)
- Julio Dominguez (Tue Aug 20 2013 - 19:12:18 PDT)
[AMBER] AMBER minimization job
- Ross Walker (Mon Aug 19 2013 - 14:05:55 PDT)
- Rejwan (Mon Aug 19 2013 - 13:58:41 PDT)
- Ross Walker (Mon Aug 19 2013 - 13:18:55 PDT)
- Rejwan (Mon Aug 19 2013 - 13:00:39 PDT)
- Ross Walker (Mon Aug 19 2013 - 12:32:13 PDT)
- David A Case (Mon Aug 19 2013 - 12:31:42 PDT)
- Rejwan (Mon Aug 19 2013 - 12:06:17 PDT)
[AMBER] amber11 installation error
- Carlos Romero (Thu Aug 29 2013 - 12:47:58 PDT)
- Carlos Romero (Thu Aug 29 2013 - 12:42:20 PDT)
- Jason Swails (Thu Aug 29 2013 - 12:29:44 PDT)
- Carlos Romero (Thu Aug 29 2013 - 11:59:23 PDT)
[AMBER] Amber12 with CUDA5.0 test results
- Soonmin Jang (Tue Aug 06 2013 - 05:44:37 PDT)
- Ross Walker (Mon Aug 05 2013 - 12:35:02 PDT)
- Soonmin Jang (Mon Aug 05 2013 - 12:06:24 PDT)
[AMBER] AMBER: antechamber error : Cannot open CONNECT.TPL, exit
- David A Case (Tue Aug 27 2013 - 06:26:37 PDT)
- glbala87.imtech.res.in (Tue Aug 27 2013 - 04:10:45 PDT)
[AMBER] AmberTools update 15 for CPPTRAJ
- Daniel Roe (Tue Aug 06 2013 - 09:14:42 PDT)
[AMBER] AmberTools13 test: possible FAILURE
- Xioling Chuang (Mon Aug 26 2013 - 21:15:27 PDT)
- Xioling Chuang (Mon Aug 26 2013 - 19:29:59 PDT)
[AMBER] ambpdb -ext ... but how?
- David A Case (Sun Aug 04 2013 - 18:01:05 PDT)
- John Gehman (Sun Aug 04 2013 - 15:13:38 PDT)
[AMBER] antechamber bond type error
- David A Case (Tue Aug 27 2013 - 06:29:34 PDT)
- glbala87.imtech.res.in (Tue Aug 27 2013 - 05:10:06 PDT)
[AMBER] antechamber returns different results from same molecule structures
- Hiromasa WATANABE (Tue Aug 27 2013 - 17:57:28 PDT)
- Hiromasa WATANABE (Tue Aug 27 2013 - 17:53:54 PDT)
- David A Case (Tue Aug 27 2013 - 06:00:04 PDT)
- Hiromasa WATANABE (Mon Aug 26 2013 - 20:14:46 PDT)
- Hiromasa WATANABE (Sun Aug 18 2013 - 17:45:04 PDT)
- Hiromasa WATANABE (Mon Aug 12 2013 - 22:33:16 PDT)
- David A Case (Mon Aug 12 2013 - 04:51:17 PDT)
- Hiromasa WATANABE (Sun Aug 11 2013 - 19:36:06 PDT)
[AMBER] ARG as a titratable residue for constant pH simulations
- Adrian Roitberg (Thu Aug 29 2013 - 07:35:50 PDT)
- Nicole Ippolito (Thu Aug 29 2013 - 07:31:23 PDT)
[AMBER] Auto-image "Could not determine atomic number from mass"
- Hailin Huang (Wed Aug 07 2013 - 12:43:28 PDT)
- Daniel Roe (Wed Aug 07 2013 - 09:11:31 PDT)
- David A Case (Tue Aug 06 2013 - 04:49:25 PDT)
- Daniel Roe (Mon Aug 05 2013 - 16:35:05 PDT)
- Hailin Huang (Mon Aug 05 2013 - 14:09:40 PDT)
- Daniel Roe (Mon Aug 05 2013 - 13:33:15 PDT)
- Hailin Huang (Mon Aug 05 2013 - 12:41:33 PDT)
[AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs
- Oliver Grant (Sat Aug 17 2013 - 05:57:04 PDT)
- Golshan Hejazi (Mon Aug 12 2013 - 06:32:20 PDT)
- Oliver Grant (Sat Aug 10 2013 - 02:26:18 PDT)
- Ross Walker (Fri Aug 09 2013 - 15:42:41 PDT)
- Golshan Hejazi (Fri Aug 09 2013 - 15:32:40 PDT)
- Golshan Hejazi (Fri Aug 09 2013 - 15:01:29 PDT)
- Ross Walker (Fri Aug 09 2013 - 14:54:37 PDT)
- Jason Swails (Fri Aug 09 2013 - 14:23:03 PDT)
- Golshan Hejazi (Fri Aug 09 2013 - 10:02:18 PDT)
- Adrian Roitberg (Fri Aug 09 2013 - 08:05:05 PDT)
- Golshan Hejazi (Fri Aug 09 2013 - 07:53:40 PDT)
- David A Case (Fri Aug 09 2013 - 06:46:51 PDT)
- Golshan Hejazi (Fri Aug 09 2013 - 06:35:55 PDT)
- Scott Le Grand (Thu Aug 08 2013 - 16:36:27 PDT)
- Ross Walker (Thu Aug 08 2013 - 12:48:19 PDT)
- Golshan Hejazi (Thu Aug 08 2013 - 12:26:53 PDT)
[AMBER] Box info not found
- David A Case (Thu Aug 15 2013 - 18:03:48 PDT)
- Rejwan (Thu Aug 15 2013 - 13:17:22 PDT)
[AMBER] can't neutralize
- David A Case (Thu Aug 01 2013 - 04:56:15 PDT)
- CH NIMILITHA Nimilitha (Thu Aug 01 2013 - 04:06:27 PDT)
[AMBER] Cannot download Amber12, bugfix.18.bz2
- Jason Swails (Fri Aug 30 2013 - 20:03:40 PDT)
- peter.stauffert.boehringer-ingelheim.com (Fri Aug 30 2013 - 12:15:02 PDT)
[AMBER] CHAMBER VDW energy in PBC
- Ross Walker (Fri Aug 30 2013 - 15:10:18 PDT)
- Jun Feng (Fri Aug 30 2013 - 14:55:30 PDT)
[AMBER] CHAMBER: dihe energy in c36 vs c22
- Ross Walker (Fri Aug 30 2013 - 15:03:47 PDT)
- Jun Feng (Fri Aug 30 2013 - 14:15:49 PDT)
[AMBER] change coordinate
- Daniel Roe (Sun Aug 04 2013 - 20:54:12 PDT)
- Vijay Manickam Achari (Sun Aug 04 2013 - 20:28:22 PDT)
[AMBER] Charmmgui pdb file error
- Giorgos Lamprinidis (Fri Aug 02 2013 - 00:22:13 PDT)
- David A Case (Thu Aug 01 2013 - 13:40:48 PDT)
- Giorgos Lamprinidis (Thu Aug 01 2013 - 07:49:38 PDT)
- David A Case (Thu Aug 01 2013 - 06:44:55 PDT)
- Giorgos Lamprinidis (Thu Aug 01 2013 - 06:17:38 PDT)
[AMBER] Chi torsions
- Steven M. Graham (Fri Aug 09 2013 - 12:49:02 PDT)
- Petr Jurecka (Fri Aug 09 2013 - 07:20:25 PDT)
- Jiri Sponer (Fri Aug 09 2013 - 02:06:43 PDT)
- Ilyas Yildirim (Thu Aug 08 2013 - 14:11:50 PDT)
- Steven M. Graham (Thu Aug 08 2013 - 13:57:43 PDT)
[AMBER] Comparing Enthalpy change and energy decomposition values
- dilrajl.bii.a-star.edu.sg (Fri Aug 23 2013 - 03:41:59 PDT)
[AMBER] Confused about Hydrogen bond and non-bond interaction.
- X Sun (Fri Aug 23 2013 - 16:50:14 PDT)
[AMBER] Constant ph with replica exchange
- Jason Swails (Thu Aug 29 2013 - 14:37:03 PDT)
- Fabrício Bracht (Thu Aug 29 2013 - 14:00:39 PDT)
[AMBER] cpptraj removes velocities upon imaging
- Daniel Roe (Sat Aug 31 2013 - 14:44:51 PDT)
- Eric Berquist (Sat Aug 31 2013 - 07:34:38 PDT)
- Daniel Roe (Sat Aug 31 2013 - 04:14:32 PDT)
- Eric Berquist (Fri Aug 30 2013 - 12:47:03 PDT)
[AMBER] cpptraj: noxcol example, order of cmdline args
- Daniel Roe (Fri Aug 09 2013 - 08:26:46 PDT)
- Jan-Philip Gehrcke (Fri Aug 09 2013 - 08:16:17 PDT)
- Daniel Roe (Fri Aug 09 2013 - 08:01:17 PDT)
- Daniel Roe (Fri Aug 09 2013 - 07:44:19 PDT)
- Jan-Philip Gehrcke (Fri Aug 09 2013 - 03:44:30 PDT)
- Jan-Philip Gehrcke (Fri Aug 09 2013 - 03:05:56 PDT)
[AMBER] Cpu busy looping?
- Jan-Philip Gehrcke (Wed Aug 21 2013 - 04:56:34 PDT)
- Jake Smith (Tue Aug 20 2013 - 17:38:37 PDT)
- Ross Walker (Tue Aug 20 2013 - 15:35:13 PDT)
- Jake Smith (Tue Aug 20 2013 - 15:19:13 PDT)
- Ross Walker (Tue Aug 20 2013 - 13:07:45 PDT)
- Jason Swails (Tue Aug 20 2013 - 13:00:56 PDT)
- Jake Smith (Tue Aug 20 2013 - 12:32:01 PDT)
[AMBER] Cterm and Nterm caps
- David A Case (Thu Aug 15 2013 - 06:16:14 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Aug 14 2013 - 23:17:12 PDT)
[AMBER] CUDA_VISIBLE_DEVICES and real instance IDs
- Ross Walker (Thu Aug 15 2013 - 13:50:48 PDT)
- Jan-Philip Gehrcke (Thu Aug 15 2013 - 12:21:09 PDT)
- Meij, Henk (Thu Aug 15 2013 - 11:47:39 PDT)
[AMBER] Density saturates at 0.97 after NPT
- Sourav Purohit (Thu Aug 22 2013 - 11:50:50 PDT)
- Ross Walker (Thu Aug 22 2013 - 11:35:38 PDT)
- Sourav Purohit (Thu Aug 22 2013 - 10:59:58 PDT)
[AMBER] dftb3
- Andreas Goetz (Wed Aug 07 2013 - 16:10:04 PDT)
- me, Nancy (Wed Aug 07 2013 - 15:26:50 PDT)
[AMBER] Difference between lower case and upper case in atomtype?
- Ross Walker (Sun Aug 11 2013 - 21:33:27 PDT)
- egeh00 (Sun Aug 11 2013 - 21:36:43 PDT)
[AMBER] Different SASA values in MM/PBSA and MM/GBSA?
- Mu Xia (Tue Aug 27 2013 - 06:32:46 PDT)
- Jason Swails (Tue Aug 27 2013 - 05:38:40 PDT)
- Mu Xia (Mon Aug 26 2013 - 20:46:29 PDT)
[AMBER] Diffusion constant's unit
- Vijay Manickam Achari (Wed Aug 07 2013 - 00:47:15 PDT)
- Ismail, Mohd F. (Tue Aug 06 2013 - 22:26:32 PDT)
- Vijay Manickam Achari (Tue Aug 06 2013 - 20:33:24 PDT)
[AMBER] Distance based mask for qmmask
- Fabrício Bracht (Fri Aug 02 2013 - 17:21:01 PDT)
- Andreas Goetz (Fri Aug 02 2013 - 10:43:32 PDT)
- Fabrício Bracht (Thu Aug 01 2013 - 21:26:22 PDT)
- Andreas Goetz (Thu Aug 01 2013 - 20:34:15 PDT)
[AMBER] Distance between group of atoms using Ptraj
- HIMANSHU JOSHI (Thu Aug 08 2013 - 23:28:16 PDT)
- David A Case (Thu Aug 08 2013 - 09:57:10 PDT)
- Daniel Roe (Thu Aug 08 2013 - 08:34:43 PDT)
- HIMANSHU JOSHI (Thu Aug 08 2013 - 03:24:28 PDT)
[AMBER] DMPC GAFF lipid membrane is freezing at 303 K.
- Dickson, Callum (Thu Aug 22 2013 - 11:13:07 PDT)
- Ross Walker (Wed Aug 21 2013 - 10:42:25 PDT)
- Subbarao Kanchi (Wed Aug 21 2013 - 06:55:27 PDT)
[AMBER] DNA Phosphate error
- David A Case (Sat Aug 10 2013 - 06:40:26 PDT)
[AMBER] Energy terms in mdout (Etot, EKtot, ...)
- José Guilherme Vilhena Albuquerque d'Orey (Sat Aug 10 2013 - 06:46:40 PDT)
- Jason Swails (Fri Aug 09 2013 - 14:15:15 PDT)
- Brian Radak (Fri Aug 09 2013 - 07:20:15 PDT)
- José Guilherme Vilhena Albuquerque d'Orey (Fri Aug 09 2013 - 03:23:00 PDT)
[AMBER] ERROR in rms: KRMS_ reported Number of atoms less than 2
- David A Case (Fri Aug 09 2013 - 06:44:00 PDT)
- Sanjib Paul (Fri Aug 09 2013 - 04:39:58 PDT)
[AMBER] Error using Antechamber
- onetwo (Mon Aug 19 2013 - 21:06:24 PDT)
- David A Case (Mon Aug 19 2013 - 06:12:09 PDT)
- onetwo (Sat Aug 17 2013 - 07:33:26 PDT)
[AMBER] Error when loading the opls dihedral information.
- David A Case (Tue Aug 06 2013 - 04:51:33 PDT)
- egeh00 (Mon Aug 05 2013 - 16:16:35 PDT)
[AMBER] error when running binding energy in amber
- nguyentb.bii.a-star.edu.sg (Thu Aug 01 2013 - 20:18:17 PDT)
- Dwight McGee (Thu Aug 01 2013 - 20:03:28 PDT)
- nguyentb.bii.a-star.edu.sg (Thu Aug 01 2013 - 19:29:40 PDT)
- nguyentb.bii.a-star.edu.sg (Thu Aug 01 2013 - 00:11:15 PDT)
[AMBER] Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM.
- Daniel Roe (Mon Aug 19 2013 - 12:00:09 PDT)
- Jason Swails (Mon Aug 19 2013 - 10:02:28 PDT)
- Thomas Evangelidis (Mon Aug 19 2013 - 05:35:36 PDT)
- Jason Swails (Sun Aug 18 2013 - 18:03:58 PDT)
- Thomas Evangelidis (Sun Aug 18 2013 - 16:17:50 PDT)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius
- WuYunjian (Wed Aug 21 2013 - 07:33:06 PDT)
- Ross Walker (Tue Aug 20 2013 - 11:30:51 PDT)
- Moacyr Comar (Tue Aug 20 2013 - 10:35:23 PDT)
- WuYunjian (Tue Aug 20 2013 - 09:13:56 PDT)
[AMBER] Forcefield for lipopeptides
- Prasanna Venkatesh D (Tue Aug 13 2013 - 00:24:04 PDT)
[AMBER] frcmod.ionsjc_*** file and water model
- Brian Radak (Thu Aug 29 2013 - 06:48:36 PDT)
- Seongeun Yang (Thu Aug 29 2013 - 04:52:08 PDT)
[AMBER] Fwd:
- Jason Swails (Wed Aug 28 2013 - 06:00:27 PDT)
- gargi borgohai (Wed Aug 28 2013 - 05:55:21 PDT)
[AMBER] Gaussian charges in xleap
- FyD (Thu Aug 29 2013 - 01:51:43 PDT)
- David A Case (Tue Aug 27 2013 - 06:24:06 PDT)
- HIMANSHU JOSHI (Tue Aug 27 2013 - 05:57:49 PDT)
- HIMANSHU JOSHI (Mon Aug 26 2013 - 22:04:34 PDT)
- FyD (Fri Aug 23 2013 - 08:47:51 PDT)
- David Case (Fri Aug 23 2013 - 07:22:45 PDT)
- HIMANSHU JOSHI (Fri Aug 23 2013 - 04:20:00 PDT)
- FyD (Thu Aug 22 2013 - 05:19:58 PDT)
- HIMANSHU JOSHI (Wed Aug 21 2013 - 22:14:43 PDT)
[AMBER] Generating snapshots in amber trajectory format
- Jason Swails (Thu Aug 01 2013 - 06:42:32 PDT)
- aneesh cna (Thu Aug 01 2013 - 03:48:03 PDT)
[AMBER] Geometricmean sigma in AMBER?
- X Sun (Tue Aug 20 2013 - 12:51:02 PDT)
[AMBER] glycam_in Xleap
- Lachele Foley (Mon Aug 26 2013 - 12:17:58 PDT)
- lara lara (Mon Aug 26 2013 - 10:22:40 PDT)
[AMBER] GpuBuffer::Download failed for kNLBuildNeighborListOrthogonal16_kernel
- Scott Le Grand (Fri Aug 09 2013 - 09:46:24 PDT)
- Scott Le Grand (Thu Aug 08 2013 - 20:10:14 PDT)
- Scott Le Grand (Thu Aug 08 2013 - 17:31:21 PDT)
- Scott Le Grand (Wed Aug 07 2013 - 10:28:58 PDT)
- Kyle Sutherland-Cash (Wed Aug 07 2013 - 10:12:59 PDT)
[AMBER] GTX-Titan / GTX780 Fix
- Ross Walker (Wed Aug 21 2013 - 10:33:20 PDT)
- iqtcub (Wed Aug 21 2013 - 01:14:06 PDT)
- Marek Maly (Wed Aug 14 2013 - 15:23:17 PDT)
- ET (Wed Aug 14 2013 - 08:07:12 PDT)
- Ross Walker (Wed Aug 07 2013 - 18:21:47 PDT)
- Divi/GMAIL (Wed Aug 07 2013 - 17:53:09 PDT)
- Ross Walker (Wed Aug 07 2013 - 10:52:51 PDT)
- Scott Le Grand (Wed Aug 07 2013 - 10:46:57 PDT)
- filip fratev (Wed Aug 07 2013 - 10:30:35 PDT)
- Ross Walker (Tue Aug 06 2013 - 10:41:04 PDT)
[AMBER] Hbond alaysis in CPPTRAJ
- Daniel Roe (Thu Aug 15 2013 - 07:37:52 PDT)
- anu chandra (Thu Aug 15 2013 - 00:10:18 PDT)
[AMBER] How to Calculate Energy
- Indrajit Deb (Fri Aug 02 2013 - 14:21:47 PDT)
- Brian Radak (Fri Aug 02 2013 - 13:12:41 PDT)
- Indrajit Deb (Fri Aug 02 2013 - 12:18:24 PDT)
[AMBER] how to check for errors in a topology library file created with saveOff
- FyD (Thu Aug 22 2013 - 05:09:01 PDT)
- Daniel Roe (Wed Aug 21 2013 - 12:01:45 PDT)
- Jose Borreguero (Wed Aug 21 2013 - 10:34:39 PDT)
- Jason Swails (Wed Aug 21 2013 - 08:29:43 PDT)
- Jose Borreguero (Wed Aug 21 2013 - 08:03:03 PDT)
- Jose Borreguero (Wed Aug 21 2013 - 07:33:07 PDT)
- FyD (Wed Aug 21 2013 - 03:54:15 PDT)
- Daniel Roe (Tue Aug 20 2013 - 20:22:50 PDT)
- Jose Borreguero (Tue Aug 20 2013 - 16:05:19 PDT)
[AMBER] How to insert a drug near center of lipids in the membrane?
- Atila Petrosian (Wed Aug 21 2013 - 01:45:04 PDT)
[AMBER] Huge improper dihedral fitting coefficient.
- Karl N. Kirschner (Wed Aug 21 2013 - 00:48:15 PDT)
- X Sun (Tue Aug 20 2013 - 12:47:29 PDT)
[AMBER] HW-HW for TIP3P?
- Brian Radak (Mon Aug 26 2013 - 13:55:18 PDT)
- X Sun (Mon Aug 26 2013 - 14:37:10 PDT)
[AMBER] Hydroxylysine Parameters
- Chris Forman (Thu Aug 29 2013 - 05:36:19 PDT)
- Chris Forman (Thu Aug 29 2013 - 05:33:45 PDT)
- FyD (Thu Aug 29 2013 - 01:47:49 PDT)
- David A Case (Tue Aug 27 2013 - 09:11:12 PDT)
- Chris Forman (Tue Aug 27 2013 - 08:23:24 PDT)
[AMBER] igb8 SURFTEN SURFOFF
- David A Case (Thu Aug 01 2013 - 04:50:16 PDT)
- berin karaman (Thu Aug 01 2013 - 00:47:28 PDT)
[AMBER] Input files for Targeted MD using Amber
- David A Case (Tue Aug 20 2013 - 18:59:29 PDT)
- Sunny Chun (Tue Aug 20 2013 - 14:39:09 PDT)
[AMBER] Is there any problem with this input file?
- Bill Miller III (Mon Aug 05 2013 - 07:47:27 PDT)
- Changqing Yan (Fri Aug 02 2013 - 07:34:03 PDT)
[AMBER] isothermal compressibility
- David A Case (Fri Aug 02 2013 - 18:27:47 PDT)
- kirtana S (Fri Aug 02 2013 - 15:42:19 PDT)
[AMBER] Jobs resubmitted when calculating entropy
- Jason Swails (Thu Aug 01 2013 - 06:54:00 PDT)
- Changqing Yan (Thu Aug 01 2013 - 03:02:50 PDT)
[AMBER] Large difference in GB and PB values of binding free energy
- Kshatresh Dutta Dubey (Sun Aug 25 2013 - 23:43:31 PDT)
- anu chandra (Sun Aug 25 2013 - 23:04:01 PDT)
[AMBER] leap question
- Raman Parkesh (Sun Aug 25 2013 - 02:40:10 PDT)
- Wang Chern Hoe (Dr) (Sun Aug 25 2013 - 00:56:49 PDT)
[AMBER] Magnesium charges using leaprc.ff99SB - metals move away
- Mallipeddi, Premalatha (Wed Aug 14 2013 - 08:38:18 PDT)
- Sorensen, Jesper (Mon Aug 12 2013 - 14:50:28 PDT)
- David A Case (Mon Aug 12 2013 - 09:10:56 PDT)
- Mallipeddi, Premalatha (Mon Aug 12 2013 - 08:40:41 PDT)
- David A Case (Fri Aug 09 2013 - 09:36:06 PDT)
- Mallipeddi, Premalatha (Fri Aug 09 2013 - 08:40:52 PDT)
- David A Case (Thu Aug 08 2013 - 18:20:54 PDT)
- Mallipeddi, Premalatha (Thu Aug 08 2013 - 14:06:42 PDT)
[AMBER] mask command issue
- Daniel Roe (Wed Aug 07 2013 - 14:00:29 PDT)
- Massimiliano Porrini (Wed Aug 07 2013 - 13:18:08 PDT)
- Daniel Roe (Wed Aug 07 2013 - 10:59:43 PDT)
- Massimiliano Porrini (Wed Aug 07 2013 - 09:30:11 PDT)
- Daniel Roe (Wed Aug 07 2013 - 08:26:33 PDT)
- Massimiliano Porrini (Wed Aug 07 2013 - 07:05:49 PDT)
[AMBER] mdout2pymbar.pl Use of uninitialized value in array element
- psu4.uic.edu (Thu Aug 22 2013 - 15:45:09 PDT)
[AMBER] MM-GBSA igb=2 or igb=5? [Ref: Exploring Protein Native States and Large-Scale Conformational Changes With a Modified Generalized Born Model]
- Jason Swails (Thu Aug 01 2013 - 06:19:57 PDT)
- Catein Catherine (Wed Jul 31 2013 - 21:09:00 PDT)
[AMBER] mmP(G)BSA correlation time
- Jason Swails (Fri Aug 30 2013 - 10:29:17 PDT)
- psu4.uic.edu (Fri Aug 30 2013 - 08:30:58 PDT)
- Jan-Philip Gehrcke (Fri Aug 30 2013 - 00:56:49 PDT)
- psu4.uic.edu (Thu Aug 29 2013 - 20:19:56 PDT)
- Jason Swails (Wed Aug 28 2013 - 04:59:54 PDT)
- psu4.uic.edu (Tue Aug 27 2013 - 16:57:16 PDT)
[AMBER] MMPBSA doubt
- Mary Varughese (Fri Aug 16 2013 - 20:34:24 PDT)
- Jason Swails (Fri Aug 16 2013 - 15:33:26 PDT)
- Mary Varughese (Thu Aug 15 2013 - 21:09:43 PDT)
- Jason Swails (Wed Aug 14 2013 - 09:11:23 PDT)
- Mary Varughese (Wed Aug 14 2013 - 03:20:47 PDT)
[AMBER] mmpbsa nonpolar contribution using stability
- wmsmith.uci.edu (Tue Aug 20 2013 - 09:19:47 PDT)
[AMBER] mmpbsa nonpolar contribution using stability calculations
- George Green (Wed Aug 21 2013 - 01:31:24 PDT)
- Jason Swails (Mon Aug 19 2013 - 04:30:53 PDT)
- George Green (Mon Aug 19 2013 - 03:07:51 PDT)
- Jason Swails (Thu Aug 01 2013 - 14:20:41 PDT)
- George Green (Thu Aug 01 2013 - 13:44:14 PDT)
- George Green (Thu Aug 01 2013 - 08:53:37 PDT)
[AMBER] MMPBSA problem
- 372133720 (Thu Aug 01 2013 - 03:54:37 PDT)
[AMBER] MMPBSA selection error
- Jason Swails (Fri Aug 09 2013 - 14:26:12 PDT)
- Hunter Brown (Fri Aug 09 2013 - 12:33:05 PDT)
- Roitberg,Adrian E (Fri Aug 09 2013 - 12:02:21 PDT)
- Bill Miller III (Fri Aug 09 2013 - 11:56:14 PDT)
- Hunter Brown (Fri Aug 09 2013 - 09:29:13 PDT)
[AMBER] MMPBSA: AttributeError: 'list' object has no attribute 'stdev'
- Xioling Chuang (Mon Aug 26 2013 - 00:37:49 PDT)
- Jason Swails (Sun Aug 25 2013 - 20:32:24 PDT)
- Xioling Chuang (Sun Aug 25 2013 - 19:23:51 PDT)
[AMBER] MMPBSA_decomp
- Jason Swails (Mon Aug 05 2013 - 22:44:29 PDT)
- 372133720 (Mon Aug 05 2013 - 18:30:02 PDT)
[AMBER] Modelling the folding of the c-terminus of a protein
- David A Case (Wed Aug 14 2013 - 04:39:55 PDT)
- Aylin Sahin (Mon Aug 12 2013 - 23:47:33 PDT)
[AMBER] mpi4py building error during AmberTools 13 install
- Jason Swails (Wed Aug 28 2013 - 07:56:41 PDT)
- sunyeping (Tue Aug 27 2013 - 02:56:58 PDT)
[AMBER] MTKPP/MCPB charge is not integer
- Jia Xu (Wed Aug 14 2013 - 11:25:58 PDT)
[AMBER] multiple heat baths in a single simulation
- James W. Snyder, Jr. (Wed Aug 07 2013 - 14:03:21 PDT)
- James W. Snyder, Jr. (Wed Aug 07 2013 - 11:38:14 PDT)
[AMBER] NAB transformation matrix conventions (rotation about x-axis is left handed?)
- Chaitanya Murthy (Mon Aug 26 2013 - 19:15:52 PDT)
[AMBER] Nmode question
- David A Case (Mon Aug 05 2013 - 11:08:08 PDT)
- David A Case (Mon Aug 05 2013 - 08:49:02 PDT)
- Changqing Yan (Mon Aug 05 2013 - 01:57:25 PDT)
[AMBER] NMR restraints not working with pmemd.cuda.parallel
- Ross Walker (Wed Aug 07 2013 - 10:38:31 PDT)
- Kyle Sutherland-Cash (Wed Aug 07 2013 - 10:07:17 PDT)
[AMBER] nmr upper_bond criteria
- David A. Case (Thu Aug 22 2013 - 19:12:52 PDT)
- sangita.imtech.res.in (Thu Aug 22 2013 - 04:57:35 PDT)
- Jason Swails (Wed Aug 21 2013 - 05:03:48 PDT)
- sangita.imtech.res.in (Tue Aug 20 2013 - 22:27:53 PDT)
[AMBER] no CMAP information written out by chamber
- ymei (Fri Aug 16 2013 - 16:31:27 PDT)
- ymei (Fri Aug 16 2013 - 10:47:53 PDT)
[AMBER] not able to build prmtop and inpcrd with glycam
- Lachele Foley (Thu Aug 22 2013 - 12:10:41 PDT)
- lara lara (Thu Aug 22 2013 - 12:07:56 PDT)
- Lachele Foley (Thu Aug 22 2013 - 12:03:42 PDT)
- lara lara (Thu Aug 22 2013 - 11:58:09 PDT)
- Lachele Foley (Thu Aug 22 2013 - 11:56:24 PDT)
- lara lara (Thu Aug 22 2013 - 11:29:23 PDT)
[AMBER] Number of contacts
- Daniel Roe (Tue Aug 27 2013 - 09:57:24 PDT)
- anu chandra (Sun Aug 25 2013 - 23:20:34 PDT)
- Daniel Roe (Fri Aug 23 2013 - 08:35:30 PDT)
- anu chandra (Fri Aug 23 2013 - 05:44:09 PDT)
[AMBER] Often, Amber BMT doesn't finish properly with Malti-GPGPU. (pmemd.cuda.MPI problem)
- Nakashima, Yoshihisa (Fri Aug 16 2013 - 01:16:24 PDT)
[AMBER] output nuclear force and hessian
- John Travers (Sat Aug 10 2013 - 15:38:05 PDT)
- David A Case (Sat Aug 10 2013 - 06:30:54 PDT)
- John Travers (Fri Aug 09 2013 - 20:01:38 PDT)
- John Travers (Wed Aug 07 2013 - 12:29:09 PDT)
- Jason Swails (Wed Aug 07 2013 - 11:41:41 PDT)
- David A Case (Tue Aug 06 2013 - 13:04:04 PDT)
- Jason Swails (Tue Aug 06 2013 - 11:45:09 PDT)
- John Travers (Tue Aug 06 2013 - 08:47:03 PDT)
- John Travers (Tue Aug 06 2013 - 08:26:33 PDT)
- Brian Radak (Tue Aug 06 2013 - 07:25:43 PDT)
- Jason Swails (Mon Aug 05 2013 - 22:41:56 PDT)
- John Travers (Mon Aug 05 2013 - 15:26:41 PDT)
- Brian Radak (Mon Aug 05 2013 - 12:20:19 PDT)
- John Travers (Mon Aug 05 2013 - 11:51:53 PDT)
[AMBER] PARALLEL PERFORMANCE OF AMBER12
- Ross Walker (Fri Aug 16 2013 - 09:52:53 PDT)
- Uday Midya (Fri Aug 16 2013 - 05:40:25 PDT)
- Ross Walker (Thu Aug 15 2013 - 22:33:05 PDT)
- Uday Midya (Thu Aug 15 2013 - 21:53:16 PDT)
[AMBER] Parameter file is not saved - AMBER!
- David A Case (Mon Aug 05 2013 - 11:11:25 PDT)
- Daniel Roe (Mon Aug 05 2013 - 09:16:47 PDT)
- Krati Sharma (Mon Aug 05 2013 - 08:54:03 PDT)
[AMBER] parmed.py with closest command from ptraj
- Jason Swails (Tue Aug 06 2013 - 11:47:21 PDT)
- Daniel Roe (Tue Aug 06 2013 - 05:51:54 PDT)
- Daniel Roe (Tue Aug 06 2013 - 05:50:33 PDT)
- Andre C. Stiel (Tue Aug 06 2013 - 03:39:39 PDT)
[AMBER] Partial Charges in AMBE force field
- FyD (Sun Aug 18 2013 - 08:29:35 PDT)
- BERGY (Fri Aug 16 2013 - 23:07:53 PDT)
[AMBER] Phosphate (-1 and -2) parameterization and Wolf2Pack
- Julio Dominguez (Mon Aug 26 2013 - 20:06:40 PDT)
- Karl N. Kirschner (Fri Aug 23 2013 - 06:39:23 PDT)
- Karl N. Kirschner (Fri Aug 23 2013 - 06:32:23 PDT)
[AMBER] PLP- L Histidinal Phosphate parameters
- David A Case (Wed Aug 21 2013 - 06:14:00 PDT)
- madhu malar (Tue Aug 20 2013 - 23:50:30 PDT)
[AMBER] PLP-L Histidinal Phosphate parameters
- FyD (Wed Aug 21 2013 - 03:50:15 PDT)
- monica.imtech.res.in (Tue Aug 20 2013 - 20:53:41 PDT)
- madhu malar (Tue Aug 20 2013 - 02:20:35 PDT)
[AMBER] PMEMD Performance issue on AMD cluster
- Jan-Philip Gehrcke (Wed Aug 21 2013 - 05:40:41 PDT)
- Jason Swails (Wed Aug 21 2013 - 05:20:14 PDT)
- Sangeetha B (Tue Aug 20 2013 - 22:29:58 PDT)
[AMBER] pmemd.cuda.MPI problem
- Ross Walker (Wed Aug 07 2013 - 13:02:50 PDT)
- Victor Ma (Wed Aug 07 2013 - 12:51:45 PDT)
- Jason Swails (Wed Aug 07 2013 - 12:44:52 PDT)
- Victor Ma (Wed Aug 07 2013 - 12:37:50 PDT)
- David A Case (Wed Aug 07 2013 - 11:50:02 PDT)
- Jason Swails (Wed Aug 07 2013 - 11:38:26 PDT)
- Victor Ma (Wed Aug 07 2013 - 09:59:24 PDT)
[AMBER] Possibility of mixing OPLS and Glycam?
- Lachele Foley (Tue Aug 13 2013 - 09:04:23 PDT)
- egeh00 (Mon Aug 12 2013 - 21:15:38 PDT)
[AMBER] Problem in energy decomposition
- Bill Miller III (Tue Aug 13 2013 - 20:57:54 PDT)
- Kshatresh Dutta Dubey (Tue Aug 13 2013 - 07:45:31 PDT)
[AMBER] problem installin amber9 in ubuntu 12.04
- Rodrigo Salazar (Sat Aug 31 2013 - 20:00:32 PDT)
[AMBER] Problem with Amber tutorial A.15
- Daniel Roe (Wed Aug 14 2013 - 15:25:23 PDT)
- Moacyr Comar (Wed Aug 14 2013 - 11:08:36 PDT)
- Jason Swails (Wed Aug 14 2013 - 09:17:33 PDT)
- Daniel Roe (Wed Aug 14 2013 - 09:05:58 PDT)
- Moacyr Comar (Wed Aug 14 2013 - 08:59:31 PDT)
- David A Case (Mon Aug 12 2013 - 07:04:13 PDT)
- Moacyr Comar (Mon Aug 12 2013 - 06:32:46 PDT)
[AMBER] problem with ambertools test
- David A. Case (Thu Aug 22 2013 - 19:06:54 PDT)
- Jason Swails (Sun Aug 18 2013 - 18:07:31 PDT)
- Majid Taghdir (Sat Aug 17 2013 - 05:22:01 PDT)
[AMBER] problem with making a movie
- MOHD HOMAIDUR RAHMAN (Thu Aug 29 2013 - 00:18:14 PDT)
- Aylin Sahin (Wed Aug 28 2013 - 23:04:27 PDT)
[AMBER] Problem with xLeap : Segmentation fault (core dumped)
- HIMANSHU JOSHI (Wed Aug 14 2013 - 09:28:15 PDT)
- David A Case (Wed Aug 14 2013 - 06:06:57 PDT)
- Hailin Huang (Wed Aug 14 2013 - 01:21:42 PDT)
- HIMANSHU JOSHI (Wed Aug 14 2013 - 00:55:54 PDT)
[AMBER] Problematic structure after minimization on GPU
- Jan-Philip Gehrcke (Tue Aug 27 2013 - 02:13:11 PDT)
- Scott Le Grand (Mon Aug 26 2013 - 10:05:01 PDT)
- Ross Walker (Mon Aug 26 2013 - 08:15:02 PDT)
- Daniel Roe (Mon Aug 26 2013 - 08:15:31 PDT)
- Jan-Philip Gehrcke (Mon Aug 26 2013 - 07:48:52 PDT)
- Jan-Philip Gehrcke (Mon Aug 26 2013 - 07:25:00 PDT)
- Ross Walker (Mon Aug 26 2013 - 07:18:59 PDT)
- Jan-Philip Gehrcke (Mon Aug 26 2013 - 04:52:27 PDT)
[AMBER] Problems running NAB scripts in the manual
- David A Case (Fri Aug 09 2013 - 10:22:53 PDT)
[AMBER] problems with calculation continuing
- Brian Radak (Mon Aug 19 2013 - 09:47:31 PDT)
- Карлов Дмитрий (Mon Aug 19 2013 - 09:11:52 PDT)
[AMBER] problems with disulfide bond creation
- case (Tue Aug 27 2013 - 19:03:27 PDT)
- kurisaki (Tue Aug 27 2013 - 18:51:00 PDT)
- sunyeping (Tue Aug 27 2013 - 18:42:43 PDT)
[AMBER] Problems with NAB
- Alexander Button (Wed Jul 31 2013 - 20:27:56 PDT)
- Alexander Button (Wed Jul 31 2013 - 19:03:54 PDT)
[AMBER] ptraj is not splitting LES trajectory
- James W. Snyder, Jr. (Sun Aug 11 2013 - 12:43:47 PDT)
- Daniel Roe (Sun Aug 11 2013 - 11:20:19 PDT)
- James W. Snyder, Jr. (Fri Aug 09 2013 - 18:09:17 PDT)
- Daniel Roe (Fri Aug 09 2013 - 17:59:12 PDT)
- James W. Snyder, Jr. (Fri Aug 09 2013 - 17:02:21 PDT)
[AMBER] Pucker Command In Cpptraj
- Daniel Roe (Mon Aug 26 2013 - 14:06:59 PDT)
- mish (Mon Aug 26 2013 - 13:14:15 PDT)
- arundhati dutta (Mon Aug 26 2013 - 12:46:30 PDT)
- Daniel Roe (Mon Aug 26 2013 - 12:42:36 PDT)
- Hamed S. Hayatshahi (Mon Aug 26 2013 - 11:55:54 PDT)
- arundhati dutta (Mon Aug 26 2013 - 09:31:29 PDT)
[AMBER] Puzzles about SCEE and SCNB?
- Jason Swails (Fri Aug 09 2013 - 15:35:46 PDT)
- egeh00 (Fri Aug 09 2013 - 14:54:33 PDT)
[AMBER] Query regarding membrane-peptide simulation
- Ross Walker (Mon Aug 19 2013 - 08:41:59 PDT)
- Aditya Padhi (Mon Aug 19 2013 - 03:28:16 PDT)
[AMBER] question about amber installation
- Jason Swails (Fri Aug 30 2013 - 05:35:59 PDT)
- Atila Petrosian (Fri Aug 30 2013 - 05:22:17 PDT)
[AMBER] Question about different SCEE&SCNB to specified atom pairs.
- Jason Swails (Tue Aug 20 2013 - 08:34:41 PDT)
- egeh00 (Tue Aug 20 2013 - 09:16:39 PDT)
- Ross Walker (Mon Aug 19 2013 - 21:19:25 PDT)
- egeh00 (Mon Aug 19 2013 - 21:45:21 PDT)
[AMBER] Question regarding H-bond calculation
- anu chandra (Tue Aug 13 2013 - 23:21:48 PDT)
- Daniel Roe (Tue Aug 13 2013 - 07:24:24 PDT)
- Kshatresh Dutta Dubey (Tue Aug 13 2013 - 01:05:01 PDT)
- anu chandra (Mon Aug 12 2013 - 23:37:54 PDT)
[AMBER] Question regarding principal component analysis
- Puspita Halder (Wed Aug 28 2013 - 23:26:00 PDT)
[AMBER] Questions about improper dihedral scan?
- Steven M. Graham (Tue Aug 06 2013 - 18:27:53 PDT)
- egeh00 (Tue Aug 06 2013 - 15:44:21 PDT)
[AMBER] R.E.D server output files
- Ayesha Fatima (Sat Aug 10 2013 - 19:33:56 PDT)
- FyD (Thu Aug 08 2013 - 03:18:43 PDT)
- Ayesha Fatima (Tue Aug 06 2013 - 19:16:09 PDT)
[AMBER] radii effect on PB_cavity surften_cavity offset
- berin karaman (Fri Aug 02 2013 - 00:24:37 PDT)
- Ray Luo, Ph.D. (Thu Aug 01 2013 - 20:36:09 PDT)
- berin karaman (Thu Aug 01 2013 - 06:54:15 PDT)
[AMBER] Reading velocity trajectories
- Daniel Roe (Sat Aug 10 2013 - 22:19:37 PDT)
- Ganesh Kamath (Fri Aug 09 2013 - 18:05:53 PDT)
[AMBER] reax forcefield
- Ross Walker (Wed Aug 07 2013 - 10:35:28 PDT)
- Yeng-Tseng Wang (Wed Aug 07 2013 - 09:45:23 PDT)
- erik.laurini.di3.units.it (Wed Aug 07 2013 - 08:42:14 PDT)
[AMBER] RED: charge equivalencing with intramolecular charge constraints?
- FyD (Sat Aug 24 2013 - 08:45:24 PDT)
- Brian Radak (Fri Aug 23 2013 - 09:21:29 PDT)
- FyD (Fri Aug 23 2013 - 09:16:05 PDT)
- Brian Radak (Fri Aug 23 2013 - 08:08:21 PDT)
[AMBER] Residue decomposition: not possible with PB ?
- Jagur Lambix (Fri Aug 09 2013 - 16:04:06 PDT)
[AMBER] Resp charges
- FyD (Thu Aug 08 2013 - 02:47:42 PDT)
- Hamed S. Hayatshahi (Mon Aug 05 2013 - 13:55:43 PDT)
- ymei (Mon Aug 05 2013 - 12:11:38 PDT)
- Morteza Chehel Amirani (Mon Aug 05 2013 - 12:03:07 PDT)
[AMBER] rk2 and rk3 values in NMR restraints
- Bharatham, Nagakumar (Wed Aug 21 2013 - 14:31:17 PDT)
[AMBER] RMSD calculation followed by superimposition
- Daniel Roe (Fri Aug 23 2013 - 08:30:51 PDT)
- moitrayee.mbu.iisc.ernet.in (Thu Aug 22 2013 - 19:25:52 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Aug 21 2013 - 23:42:35 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Aug 21 2013 - 23:42:09 PDT)
- Bill Ross (Wed Aug 21 2013 - 22:04:00 PDT)
- Daniel Roe (Wed Aug 21 2013 - 22:02:37 PDT)
- Daniel Roe (Wed Aug 21 2013 - 21:59:09 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Aug 21 2013 - 22:01:43 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Aug 21 2013 - 21:53:15 PDT)
- Daniel Roe (Wed Aug 21 2013 - 21:22:05 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Aug 21 2013 - 18:25:19 PDT)
- Jan-Philip Gehrcke (Thu Aug 15 2013 - 01:27:07 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Aug 14 2013 - 19:34:39 PDT)
[AMBER] sander option "-radii"
- Soonmin Jang (Tue Aug 06 2013 - 05:48:49 PDT)
[AMBER] SASA
- Jason Swails (Tue Aug 20 2013 - 06:12:30 PDT)
- fatahiya (Tue Aug 20 2013 - 01:27:57 PDT)
[AMBER] SASA / AmberTools1.5
- Daniel Roe (Thu Aug 01 2013 - 21:38:10 PDT)
- fatahiya (Thu Aug 01 2013 - 19:23:13 PDT)
- David A Case (Thu Aug 01 2013 - 04:52:09 PDT)
- fatahiya (Thu Aug 01 2013 - 02:44:52 PDT)
[AMBER] Secondary Structure analysis
- Daniel Roe (Wed Aug 07 2013 - 10:16:50 PDT)
- Chinthaka Ratnaweera (Wed Aug 07 2013 - 09:56:09 PDT)
[AMBER] Segmentation Fault
- David A Case (Tue Aug 06 2013 - 06:39:21 PDT)
- Souvik Sur (Tue Aug 06 2013 - 05:59:28 PDT)
- David A Case (Tue Aug 06 2013 - 04:53:31 PDT)
- Souvik Sur (Mon Aug 05 2013 - 22:41:08 PDT)
[AMBER] setbox command
- Vijay Manickam Achari (Sun Aug 04 2013 - 21:10:53 PDT)
[AMBER] setting up a covalently bonded ligand to enzyme with tleap
- David A Case (Wed Aug 28 2013 - 05:33:18 PDT)
- Mahmoud Soliman (Wed Aug 28 2013 - 00:46:30 PDT)
[AMBER] setting up non-standard amino acid residues for MD simulation
- Suri Moonsamy (Mon Aug 05 2013 - 02:22:43 PDT)
[AMBER] Simmetry problem
- Jason Swails (Thu Aug 29 2013 - 04:54:44 PDT)
- Rodrigo Salazar (Wed Aug 28 2013 - 18:51:20 PDT)
[AMBER] Simulating two hosts together
- marawan hussain (Thu Aug 29 2013 - 03:30:35 PDT)
[AMBER] simulation of single strand DNA
- David A Case (Tue Aug 13 2013 - 11:59:31 PDT)
- Collins Nganou (Tue Aug 13 2013 - 09:19:19 PDT)
[AMBER] SLipids force field with AMBER12
- Thomas Evangelidis (Wed Aug 21 2013 - 06:41:24 PDT)
[AMBER] Suggestions for using
- Hunter Brown (Thu Aug 08 2013 - 14:44:30 PDT)
[AMBER] Suggestions for using "distance" in cpptraj
- Daniel Roe (Thu Aug 08 2013 - 14:29:24 PDT)
- Hunter Brown (Thu Aug 08 2013 - 13:44:57 PDT)
[AMBER] Terminal pair fraying in nucleic acids
- David A Case (Fri Aug 02 2013 - 10:10:48 PDT)
- Asmita Gupta (Fri Aug 02 2013 - 05:45:42 PDT)
- David A Case (Fri Aug 02 2013 - 05:24:31 PDT)
- Asmita Gupta (Thu Aug 01 2013 - 22:46:03 PDT)
[AMBER] TI input files in A9 tutorial and Amber12 manual
- David A Case (Fri Aug 30 2013 - 12:45:01 PDT)
- Hamed S. Hayatshahi (Fri Aug 30 2013 - 11:14:17 PDT)
[AMBER] TI with ifsc==2 (reposted)
- Kepa K. Burusco (Fri Aug 09 2013 - 11:45:24 PDT)
- steinbrt.rci.rutgers.edu (Fri Aug 09 2013 - 08:46:44 PDT)
- David A Case (Fri Aug 09 2013 - 08:30:57 PDT)
- Kepa K. Burusco (Fri Aug 09 2013 - 08:01:06 PDT)
[AMBER] total charge of the ligand
- Mary Varughese (Fri Aug 23 2013 - 23:20:53 PDT)
[AMBER] Trajectory post-processing
- VanDyne_Aaron (Sat Aug 10 2013 - 17:52:44 PDT)
- Daniel Roe (Sat Aug 10 2013 - 14:09:38 PDT)
- Daniel Roe (Fri Aug 09 2013 - 08:28:32 PDT)
- VanDyne_Aaron (Thu Aug 08 2013 - 09:48:09 PDT)
- Daniel Roe (Thu Aug 08 2013 - 08:27:08 PDT)
- VanDyne_Aaron (Thu Aug 08 2013 - 07:39:01 PDT)
- Jason Swails (Tue Aug 06 2013 - 17:13:09 PDT)
- VanDyne_Aaron (Tue Aug 06 2013 - 14:59:21 PDT)
- VanDyne_Aaron (Tue Aug 06 2013 - 14:57:27 PDT)
- Daniel Roe (Tue Aug 06 2013 - 14:08:02 PDT)
- Brian Radak (Tue Aug 06 2013 - 14:06:38 PDT)
- VanDyne_Aaron (Tue Aug 06 2013 - 13:50:55 PDT)
[AMBER] Tutorial for specified SCEE and SCNB for different atom pairs?
- Ross Walker (Fri Aug 16 2013 - 21:25:15 PDT)
- Ross Walker (Fri Aug 16 2013 - 21:12:39 PDT)
- egeh00 (Fri Aug 16 2013 - 21:31:58 PDT)
[AMBER] Two questions in one...
- Daniel Roe (Mon Aug 19 2013 - 13:13:02 PDT)
- Karl N. Kirschner (Mon Aug 19 2013 - 00:27:40 PDT)
- Julio Dominguez (Sun Aug 18 2013 - 20:43:52 PDT)
[AMBER] Updating AmberTools1.5
- Daniel Roe (Thu Aug 01 2013 - 21:40:39 PDT)
- fatahiya (Thu Aug 01 2013 - 19:49:36 PDT)
[AMBER] Using ante-mmpbsa.py to create prmtops
- Jason Swails (Sat Aug 03 2013 - 06:47:17 PDT)
- Daniel Roe (Fri Aug 02 2013 - 11:00:33 PDT)
- Hunter Brown (Fri Aug 02 2013 - 10:39:47 PDT)
- Daniel Roe (Fri Aug 02 2013 - 10:20:52 PDT)
- Hunter Brown (Fri Aug 02 2013 - 10:17:34 PDT)
- Jason Swails (Thu Aug 01 2013 - 14:16:21 PDT)
- Hunter Brown (Thu Aug 01 2013 - 14:05:09 PDT)
- Jason Swails (Thu Aug 01 2013 - 11:14:00 PDT)
- Hunter Brown (Thu Aug 01 2013 - 10:07:36 PDT)
[AMBER] which energy terms are included in TI DV/DL and why it fluctuate so wildly?
- steinbrt.rci.rutgers.edu (Tue Aug 13 2013 - 01:35:50 PDT)
- psu4.uic.edu (Mon Aug 12 2013 - 21:26:23 PDT)
[AMBER] Why are sigma values of OPLS so big?
- David A Case (Thu Aug 08 2013 - 18:33:07 PDT)
- egeh00 (Thu Aug 08 2013 - 14:10:36 PDT)
[AMBER] xLeap : Undo option
- HIMANSHU JOSHI (Thu Aug 29 2013 - 11:10:22 PDT)
[AMBER] σ in Amber and OPLS-AA?
- Jason Swails (Thu Aug 22 2013 - 19:16:52 PDT)
- X Sun (Thu Aug 22 2013 - 16:53:27 PDT)
[AMBER] 答复: problems with disulfide bond creation
- sunyeping (Wed Aug 28 2013 - 17:09:07 PDT)
Magnesium charges using leaprc.ff99SB - metals move away
- Mallipeddi, Premalatha (Wed Aug 14 2013 - 15:41:45 PDT)
MMPBSA problem
- Gannett, Peter (Thu Aug 01 2013 - 06:21:30 PDT)
- Jason Swails (Thu Aug 01 2013 - 06:22:33 PDT)
- 372133720 (Thu Aug 01 2013 - 05:57:41 PDT)
- 372133720 (Wed Jul 31 2013 - 19:01:51 PDT)
output nuclear force and hessian
- David A Case (Sat Aug 10 2013 - 18:55:07 PDT)
- John Travers (Sat Aug 10 2013 - 15:02:26 PDT)

Amber Archive Aug 2013 by subject