Amber Archive Mar 2008: by subject

AMBER:
- Jianyin Shao (Thu Mar 06 2008 - 13:24:03 PST)
- Ross Walker (Thu Mar 06 2008 - 10:37:16 PST)
- Steve Seibold (Thu Mar 06 2008 - 10:27:34 PST)
- Thomas Steinbrecher (Thu Mar 06 2008 - 10:13:23 PST)
- Steve Seibold (Thu Mar 06 2008 - 10:04:01 PST)
AMBER: [success] problem compiling Amber9 on Bull Linux
- Yannick Monclin (Thu Mar 13 2008 - 04:56:48 PDT)
AMBER: a minor bug in RESP
- Ye Mei (Tue Mar 18 2008 - 00:05:34 PDT)
AMBER: a question about parameter b in the hyperbolic form of penalty function for RESP fit
- Ye Mei (Wed Mar 05 2008 - 01:30:50 PST)
AMBER: ACS COMP Division awards- deadline this week
- Carlos Simmerling (Mon Mar 03 2008 - 16:14:03 PST)
AMBER: Adding New Parameters and Modifying Existing Parameters
- Thomas Steinbrecher (Tue Mar 11 2008 - 09:46:33 PDT)
- serhanyigen.mail.ege.edu.tr (Tue Mar 11 2008 - 04:51:18 PDT)
AMBER: addions and addions2
- Bill Ross (Tue Mar 25 2008 - 10:34:52 PDT)
- dpandit.brandeis.edu (Tue Mar 25 2008 - 07:38:22 PDT)
AMBER: Amber 8 Equivalent of the Amber 5 - Edit program
- Mohd Farid Ismail (Tue Mar 04 2008 - 17:09:52 PST)
AMBER: AMBER 9 testing
- David A. Case (Sun Mar 30 2008 - 09:23:15 PDT)
- Taufik Al-Sarraj (Fri Mar 28 2008 - 21:13:31 PDT)
- David A. Case (Fri Mar 28 2008 - 17:10:02 PDT)
- Taufik Al-Sarraj (Fri Mar 28 2008 - 17:18:30 PDT)
AMBER: AMBER install problem
- Kijeong Kwac (Thu Mar 13 2008 - 10:35:10 PDT)
- David A. Case (Tue Mar 11 2008 - 17:47:58 PDT)
- Atro Tossavainen (Mon Mar 10 2008 - 23:51:18 PDT)
- David A. Case (Mon Mar 10 2008 - 17:50:30 PDT)
AMBER: Amber Workshop
- Chih-Ying Lin (Mon Mar 31 2008 - 13:40:52 PDT)
- Chih-Ying Lin (Fri Mar 28 2008 - 22:58:14 PDT)
AMBER: Amber9 Installation Problem
- David A. Case (Thu Mar 20 2008 - 16:23:53 PDT)
- trudy.uoguelph.ca (Thu Mar 20 2008 - 15:51:08 PDT)
- trudy.uoguelph.ca (Thu Mar 20 2008 - 15:43:48 PDT)
- David A. Case (Wed Mar 19 2008 - 18:37:57 PDT)
- Cenk Andac (Wed Mar 19 2008 - 13:55:23 PDT)
- Cenk Andac (Wed Mar 19 2008 - 13:43:50 PDT)
- Cenk Andac (Wed Mar 19 2008 - 13:25:25 PDT)
- trudy.uoguelph.ca (Wed Mar 19 2008 - 09:28:35 PDT)
AMBER: anion and cation simulaton
- FyD (Tue Mar 25 2008 - 12:54:56 PDT)
- gurpreet singh (Tue Mar 25 2008 - 09:22:29 PDT)
AMBER: Antechamber, net molecular charge
- Junmei Wang (Mon Mar 10 2008 - 07:39:08 PDT)
- gurpreet singh (Sun Mar 09 2008 - 21:51:58 PDT)
AMBER: Atom types/parameters for chromene
- anna.schrey.gmx.de (Thu Mar 06 2008 - 05:35:06 PST)
- David A. Case (Wed Mar 05 2008 - 11:15:25 PST)
- Francesco Pietra (Wed Mar 05 2008 - 10:07:05 PST)
- Junmei Wang (Wed Mar 05 2008 - 08:23:19 PST)
- anna.schrey.gmx.de (Wed Mar 05 2008 - 01:34:24 PST)
AMBER: Benchmarks on Fujitsu PrimePower 2500?
- Atro Tossavainen (Mon Mar 10 2008 - 06:24:33 PDT)
- Robert Duke (Mon Mar 10 2008 - 06:24:21 PDT)
- Atro Tossavainen (Mon Mar 10 2008 - 01:04:20 PDT)
- Craig Gough (Sun Mar 09 2008 - 22:36:28 PDT)
AMBER: can't make antechamber work for regular nucleotides
- Junmei Wang (Tue Mar 18 2008 - 14:08:46 PDT)
- Mey Khalili (Mon Mar 17 2008 - 06:59:01 PDT)
- Junmei Wang (Fri Mar 14 2008 - 19:10:41 PDT)
- Mey Khalili (Thu Mar 13 2008 - 07:03:45 PDT)
AMBER: Charge scheme for simulating protonated adenine
- prateeksha s (Fri Mar 21 2008 - 09:32:14 PDT)
- prateeksha s (Fri Mar 21 2008 - 09:32:06 PDT)
- rpaduri.chem.wayne.edu (Fri Mar 21 2008 - 08:29:18 PDT)
- FyD (Fri Mar 21 2008 - 00:43:51 PDT)
- prateeksha s (Thu Mar 20 2008 - 23:58:19 PDT)
AMBER: Clarification on error message
- Campbell, Patrick (Sat Mar 08 2008 - 13:15:36 PST)
- Thomas Steinbrecher (Sat Mar 08 2008 - 12:17:35 PST)
- Campbell, Patrick (Sat Mar 08 2008 - 12:09:23 PST)
AMBER: cntrl namelist error
- Campbell, Patrick (Sat Mar 22 2008 - 09:22:18 PDT)
- Campbell, Patrick (Sat Mar 22 2008 - 09:11:39 PDT)
- David A. Case (Sat Mar 22 2008 - 09:11:52 PDT)
- Ross Walker (Sat Mar 22 2008 - 09:01:47 PDT)
- Campbell, Patrick (Sat Mar 22 2008 - 08:40:16 PDT)
AMBER: Compiler issues with Altix450
- David A. Case (Mon Mar 10 2008 - 16:29:50 PDT)
- Atro Tossavainen (Mon Mar 10 2008 - 16:13:45 PDT)
- finke.oakland.edu (Mon Mar 10 2008 - 13:45:37 PDT)
- Atro Tossavainen (Sat Mar 08 2008 - 14:19:36 PST)
- finke.oakland.edu (Sat Mar 08 2008 - 10:37:25 PST)
AMBER: compiling AMBER9 with bintraj option on AMD64
- Vlad Cojocaru (Tue Mar 18 2008 - 02:32:13 PDT)
- David A. Case (Mon Mar 17 2008 - 16:48:00 PDT)
- Vlad Cojocaru (Fri Mar 14 2008 - 10:44:56 PDT)
AMBER: convert AMBER format input files into DL_POLY format input files?
- Kefa Lu (Tue Mar 11 2008 - 01:27:23 PDT)
AMBER: Convert dcd to mdcrd
- Vlad Cojocaru (Wed Mar 26 2008 - 02:02:38 PDT)
- Seth Lilavivat (Tue Mar 25 2008 - 11:13:22 PDT)
AMBER: distance restraint
- David A. Case (Thu Mar 13 2008 - 13:40:07 PDT)
- gurpreet singh (Thu Mar 13 2008 - 04:28:28 PDT)
AMBER: Energy calculation and replica exchange in Amber9
- Li Dawei (Thu Mar 13 2008 - 06:50:49 PDT)
AMBER: energy problems in simulation with restraints
- David A. Case (Mon Mar 31 2008 - 08:35:58 PDT)
- Daniel Cappel (Mon Mar 31 2008 - 02:39:13 PDT)
AMBER: equilibration of peptide
- David A. Case (Sat Mar 22 2008 - 10:51:47 PDT)
- tushar garud (Fri Mar 21 2008 - 21:02:25 PDT)
AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127
- David Rangel (Wed Mar 12 2008 - 10:04:18 PDT)
- David A. Case (Tue Mar 11 2008 - 22:43:26 PDT)
- David Rangel (Tue Mar 11 2008 - 20:30:14 PDT)
AMBER: Error with a binary restart file
- David A. Case (Wed Mar 26 2008 - 18:11:58 PDT)
- Kijeong Kwac (Wed Mar 26 2008 - 16:07:51 PDT)
AMBER: Error- MM_PBSA calculation
- vikky 99 (Thu Mar 27 2008 - 01:47:53 PDT)
AMBER: FAD and NAD parameters
- FyD (Wed Mar 26 2008 - 03:57:27 PDT)
- Thomas Leonard (Wed Mar 26 2008 - 02:26:52 PDT)
AMBER: force field
- oguz gurbulak (Thu Mar 13 2008 - 15:00:58 PDT)
AMBER: Free energy landscape? HOWTO?
- Yi-Ming Cheng (Mon Mar 31 2008 - 01:12:05 PDT)
AMBER: Fwd: positive potential energy and large 1-4 EEL
- David A. Case (Mon Mar 10 2008 - 17:19:51 PDT)
- Mey Khalili (Fri Mar 07 2008 - 08:54:28 PST)
AMBER: GAFF
- Eric Germaneau (Fri Mar 28 2008 - 05:38:41 PDT)
AMBER: Happy holi
- Bertrand P. S. Russell (Thu Mar 20 2008 - 02:03:22 PDT)
AMBER: Heating POL3 Box Troubles
- David A. Case (Wed Mar 19 2008 - 14:57:54 PDT)
- Paul Johns (Wed Mar 19 2008 - 12:22:50 PDT)
- David A. Case (Mon Mar 17 2008 - 22:30:48 PDT)
- Paul Johns (Mon Mar 17 2008 - 13:07:02 PDT)
- David A. Case (Fri Mar 14 2008 - 21:41:09 PDT)
- David A. Case (Fri Mar 14 2008 - 20:40:35 PDT)
- Thomas Steinbrecher (Fri Mar 14 2008 - 14:22:21 PDT)
- Paul Johns (Fri Mar 14 2008 - 14:01:22 PDT)
- Thomas Steinbrecher (Fri Mar 14 2008 - 12:31:03 PDT)
- Paul Johns (Fri Mar 14 2008 - 12:13:02 PDT)
- Thomas Steinbrecher (Fri Mar 14 2008 - 12:01:06 PDT)
- Paul Johns (Fri Mar 14 2008 - 11:44:44 PDT)
AMBER: help regarding warning message
- snoze pa (Tue Mar 25 2008 - 13:23:55 PDT)
- David A. Case (Tue Mar 25 2008 - 11:51:07 PDT)
- snoze pa (Tue Mar 25 2008 - 09:17:43 PDT)
AMBER: How to calculate deformability by PTRAJ ?
- sychen (Thu Mar 13 2008 - 18:44:36 PDT)
AMBER: how to link two different atoms in xLeap
- David A. Case (Wed Mar 26 2008 - 21:52:18 PDT)
- snoze pa (Wed Mar 26 2008 - 13:56:12 PDT)
AMBER: hybrid remd imaging
- Geoff Wood (Thu Mar 27 2008 - 05:56:30 PDT)
- Geoff Wood (Mon Mar 24 2008 - 09:21:41 PDT)
- Geoff Wood (Mon Mar 24 2008 - 09:16:25 PDT)
- Carlos Simmerling (Mon Mar 24 2008 - 08:59:24 PDT)
- Geoff Wood (Mon Mar 24 2008 - 08:51:51 PDT)
AMBER: implicit energy calculations
- Thomas Cheatham III (Thu Mar 13 2008 - 10:47:04 PDT)
- rebeca.mmb.pcb.ub.es (Thu Mar 13 2008 - 09:26:43 PDT)
AMBER: INPCRD error on open
- Campbell, Patrick (Thu Mar 20 2008 - 11:35:37 PDT)
- Campbell, Patrick (Thu Mar 20 2008 - 11:37:45 PDT)
- Carlos Simmerling (Thu Mar 20 2008 - 10:10:23 PDT)
- Campbell, Patrick (Thu Mar 20 2008 - 10:02:12 PDT)
- Cyril Bauvais (Thu Mar 20 2008 - 09:04:31 PDT)
- Carlos Simmerling (Thu Mar 20 2008 - 08:22:56 PDT)
- Campbell, Patrick (Thu Mar 20 2008 - 08:17:32 PDT)
AMBER: Inquiry on analyzing the amplitude from nmdout results
- David A. Case (Wed Mar 19 2008 - 15:49:21 PDT)
- James Thomas (Wed Mar 19 2008 - 15:00:35 PDT)
- David A. Case (Wed Mar 19 2008 - 14:46:10 PDT)
- James Thomas (Wed Mar 19 2008 - 09:09:05 PDT)
AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis
- David A. Case (Fri Mar 07 2008 - 13:36:33 PST)
- James Thomas (Fri Mar 07 2008 - 09:30:58 PST)
AMBER: installation amber9
- David A. Case (Mon Mar 31 2008 - 10:51:45 PDT)
- Geoff Wood (Mon Mar 31 2008 - 04:02:01 PDT)
AMBER: lastrst problem
- san_amber roy (Wed Mar 12 2008 - 08:07:23 PDT)
AMBER: measuring contacts: error "glibc detected"
- rebeca.mmb.pcb.ub.es (Fri Mar 28 2008 - 05:26:42 PDT)
AMBER: meet problem in adding ions and waterbox
- Emilio Xavier Esposito (Sun Mar 30 2008 - 10:26:45 PDT)
- Qiang Li (Sat Mar 29 2008 - 22:43:54 PDT)
AMBER: memory limitation of Amber 9
- David A. Case (Mon Mar 31 2008 - 22:50:41 PDT)
- yavuzturkm.prc.boun.edu.tr (Mon Mar 31 2008 - 11:49:40 PDT)
AMBER: Microcannonical MD Reference
- David A. Case (Fri Mar 07 2008 - 14:47:02 PST)
- priya priya (Fri Mar 07 2008 - 05:40:34 PST)
AMBER: missing gaff parameters
- Samuele Giani (Tue Mar 04 2008 - 08:42:03 PST)
- Ross Walker (Tue Mar 04 2008 - 07:39:03 PST)
- Junmei Wang (Tue Mar 04 2008 - 06:53:39 PST)
- Samuele Giani (Tue Mar 04 2008 - 00:46:38 PST)
AMBER: mm-pbsa multiple trajectory approach?
- Seth Lilavivat (Fri Mar 28 2008 - 08:28:31 PDT)
- Chris Moth (Wed Mar 26 2008 - 15:21:25 PDT)
- Seth Lilavivat (Wed Mar 26 2008 - 10:32:54 PDT)
AMBER: mm_pbsa positive ELE
- Ray Luo (Mon Mar 17 2008 - 13:14:57 PDT)
- Qi Yan (Mon Mar 17 2008 - 12:23:52 PDT)
- Ray Luo (Mon Mar 17 2008 - 11:33:11 PDT)
- Qi Yan (Mon Mar 17 2008 - 11:20:21 PDT)
AMBER: mmpbsa INSTRNG error?
- Gohlke.bioinformatik.uni-frankfurt.de (Sun Mar 09 2008 - 09:13:05 PDT)
- Sergio Wong (Sat Mar 08 2008 - 22:06:44 PST)
AMBER: MNDO parameters for Mg+2
- Ross Walker (Wed Mar 19 2008 - 11:10:18 PDT)
- E.M. (Wed Mar 19 2008 - 10:28:09 PDT)
AMBER: multiple dihedral restraints using group
- mkseo (Mon Mar 31 2008 - 10:11:30 PDT)
AMBER: Negative ligand
- Syed Tarique Moin (Sat Mar 15 2008 - 02:12:09 PDT)
AMBER: Negative ligand (Peroxide)
- Syed Tarique Moin (Sat Mar 08 2008 - 03:36:56 PST)
AMBER: nmode
- David A. Case (Mon Mar 31 2008 - 12:25:52 PDT)
- James Thomas (Mon Mar 31 2008 - 11:48:43 PDT)
AMBER: Nmode segmentation fault
- James Thomas (Tue Mar 25 2008 - 12:00:44 PDT)
- David A. Case (Tue Mar 25 2008 - 11:44:51 PDT)
- James Thomas (Tue Mar 25 2008 - 10:22:43 PDT)
- David A. Case (Tue Mar 25 2008 - 09:34:37 PDT)
- James Thomas (Tue Mar 25 2008 - 04:53:21 PDT)
AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER?
- Edyta Malolepsza (Mon Mar 31 2008 - 06:05:42 PDT)
- David A. Case (Wed Mar 19 2008 - 15:54:24 PDT)
- Francesco Pietra (Wed Mar 19 2008 - 10:26:24 PDT)
- Edyta Malolepsza (Wed Mar 19 2008 - 09:49:45 PDT)
- David A. Case (Wed Mar 19 2008 - 08:42:13 PDT)
- Edyta Malolepsza (Thu Mar 06 2008 - 04:23:06 PST)
AMBER: NTR Restraints
- David A. Case (Thu Mar 27 2008 - 13:17:31 PDT)
- Daniel Smith (Tue Mar 25 2008 - 18:17:27 PDT)
AMBER: NVE energy and temperature drift
- Lars Skjærven (Fri Mar 07 2008 - 09:34:33 PST)
- David A. Case (Fri Mar 07 2008 - 08:32:51 PST)
- Lars Skjærven (Fri Mar 07 2008 - 07:36:48 PST)
AMBER: OPLS force field
- David A. Case (Wed Mar 26 2008 - 09:08:57 PDT)
- aneesh cna (Wed Mar 26 2008 - 08:48:19 PDT)
AMBER: output effective Born radii
- Holly Freedman (Mon Mar 10 2008 - 19:24:32 PDT)
- David A. Case (Mon Mar 10 2008 - 17:07:39 PDT)
- Holly Freedman (Mon Mar 10 2008 - 15:57:06 PDT)
Amber: parameters for Silicon
- Scott Brozell (Mon Mar 10 2008 - 16:57:29 PDT)
AMBER: PF6 parameters
- caoch (Thu Mar 27 2008 - 21:28:03 PDT)
- aneesh cna (Wed Mar 26 2008 - 21:43:58 PDT)
AMBER: potential of mean force: Unit of PMF energies and min path
- Catein Catherine (Wed Mar 19 2008 - 22:26:43 PDT)
AMBER: Problem running implicit minimization
- Lili Peng (Tue Mar 04 2008 - 17:29:36 PST)
- Thomas Cheatham (Tue Mar 04 2008 - 15:47:50 PST)
- Carlos Simmerling (Tue Mar 04 2008 - 15:39:23 PST)
- Lili Peng (Tue Mar 04 2008 - 15:25:32 PST)
- Carlos Simmerling (Tue Mar 04 2008 - 03:04:38 PST)
- Lili Peng (Mon Mar 03 2008 - 22:17:27 PST)
- David A. Case (Mon Mar 03 2008 - 21:59:00 PST)
- Lili Peng (Mon Mar 03 2008 - 21:10:52 PST)
AMBER: problem with antech amber
- David A. Case (Fri Mar 14 2008 - 22:09:00 PDT)
- Madjid Taghdir (Mon Mar 10 2008 - 08:07:16 PDT)
AMBER: problem with distance restrain
- David A. Case (Tue Mar 18 2008 - 12:00:11 PDT)
- aneesh cna (Tue Mar 18 2008 - 03:16:09 PDT)
AMBER: problem with distance restraints
- David A. Case (Fri Mar 21 2008 - 10:56:28 PDT)
- aneesh cna (Thu Mar 20 2008 - 03:13:31 PDT)
AMBER: problem with nmod
- David A. Case (Fri Mar 28 2008 - 17:19:40 PDT)
- yuri pomè (Fri Mar 28 2008 - 09:42:54 PDT)
AMBER: Problems with neglected restaints
- anna.schrey.gmx.de (Thu Mar 20 2008 - 12:43:20 PDT)
- David A. Case (Tue Mar 18 2008 - 10:15:56 PDT)
- Carlos Simmerling (Tue Mar 18 2008 - 10:05:11 PDT)
- anna.schrey.gmx.de (Tue Mar 18 2008 - 09:40:20 PDT)
AMBER: Protein rotating out of box
- Lars Skjærven (Thu Mar 27 2008 - 14:34:48 PDT)
AMBER: protonated histidine ( charges in parm file versus all_a mino03.lib ). . .
- Lwin, ThuZar (Tue Mar 18 2008 - 09:45:49 PDT)
AMBER: protonated histidine ( charges in parm file versus all_amino03.lib )
- Lwin, ThuZar (Thu Mar 13 2008 - 17:13:57 PDT)
AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ).
- Ross Walker (Fri Mar 14 2008 - 09:30:13 PDT)
- Lwin, ThuZar (Fri Mar 14 2008 - 08:32:25 PDT)
AMBER: ptraj and non-bonded contacts
- Samuel Genheden (a03samge) (Wed Mar 12 2008 - 09:34:44 PDT)
AMBER: ptraj, hbond and non-bonded contacts
- Jojart Balazs (Fri Mar 14 2008 - 01:19:37 PDT)
- Thomas Cheatham III (Thu Mar 13 2008 - 10:49:14 PDT)
- Samuel Genheden (a03samge) (Thu Mar 13 2008 - 07:54:03 PDT)
AMBER: question on antechamber: jaguar ouput
- wei zhang (Wed Mar 12 2008 - 11:14:55 PDT)
- Marcelo Puiatti (Tue Mar 11 2008 - 11:35:10 PDT)
- Junmei Wang (Tue Mar 11 2008 - 11:22:52 PDT)
- wei zhang (Tue Mar 11 2008 - 10:01:55 PDT)
AMBER: questions about run MD at different pH
- David A. Case (Tue Mar 04 2008 - 17:59:49 PST)
- Kailee (Tue Mar 04 2008 - 03:40:30 PST)
- David A. Case (Mon Mar 03 2008 - 21:07:00 PST)
- Kailee (Mon Mar 03 2008 - 06:51:40 PST)
AMBER: Questions toward Azobenzene
- Chih-Ying Lin (Thu Mar 27 2008 - 21:23:40 PDT)
AMBER: reg molecular dynamics
- Uma R (Fri Mar 07 2008 - 19:17:32 PST)
AMBER: Regarding SHAKE
- gurpreet singh (Sun Mar 30 2008 - 03:38:48 PDT)
AMBER: regarding:calculation of b factor using ptraj
- gurpreet singh (Sun Mar 02 2008 - 09:24:29 PST)
- jani sahil (Sat Mar 01 2008 - 08:10:10 PST)
AMBER: REMD simulation error
- Guillaume Renvez (Fri Mar 28 2008 - 07:01:20 PDT)
AMBER: replica exchange : problem with sander
- Guillaume Renvez (Thu Mar 20 2008 - 08:02:29 PDT)
- Carlos Simmerling (Thu Mar 20 2008 - 07:47:32 PDT)
- Guillaume Renvez (Wed Mar 19 2008 - 06:57:55 PDT)
- Carlos Simmerling (Wed Mar 19 2008 - 06:49:23 PDT)
- Guillaume Renvez (Wed Mar 19 2008 - 06:35:55 PDT)
- Carlos Simmerling (Wed Mar 19 2008 - 06:25:11 PDT)
- Guillaume Renvez (Wed Mar 19 2008 - 06:13:01 PDT)
- Carlos Simmerling (Wed Mar 19 2008 - 05:47:04 PDT)
- Guillaume Renvez (Wed Mar 19 2008 - 05:14:38 PDT)
- Guillaume Renvez (Tue Mar 18 2008 - 10:24:10 PDT)
- Carlos Simmerling (Tue Mar 18 2008 - 10:12:03 PDT)
- Guillaume Renvez (Tue Mar 18 2008 - 10:07:54 PDT)
- Carlos Simmerling (Tue Mar 18 2008 - 09:39:01 PDT)
- Guillaume Renvez (Tue Mar 18 2008 - 09:21:21 PDT)
- Guillaume Renvez (Tue Mar 18 2008 - 08:29:39 PDT)
- Carlos Simmerling (Tue Mar 18 2008 - 07:29:38 PDT)
- Guillaume Renvez (Tue Mar 18 2008 - 07:09:34 PDT)
AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water
- Markus Kaukonen (Sun Mar 30 2008 - 23:34:48 PDT)
AMBER: residual dipolar couplings - alignment tensor energy
- Douglas Kojetin (Wed Mar 26 2008 - 12:46:48 PDT)
AMBER: RMSD of two different molecules
- JunJun Liu (Wed Mar 26 2008 - 14:54:11 PDT)
- Da-Wei Li (Wed Mar 26 2008 - 13:39:19 PDT)
- JunJun Liu (Wed Mar 26 2008 - 13:35:32 PDT)
AMBER: running minimisation on cis-azobenzene
- Thomas Steinbrecher (Mon Mar 31 2008 - 13:14:17 PDT)
- Chih-Ying Lin (Mon Mar 31 2008 - 12:45:20 PDT)
AMBER: Select specific residues (leap)
- FyD (Mon Mar 31 2008 - 06:32:30 PDT)
- Marta Rossini (Mon Mar 31 2008 - 05:57:04 PDT)
- FyD (Mon Mar 31 2008 - 04:19:49 PDT)
- Marta Rossini (Mon Mar 31 2008 - 04:00:52 PDT)
- FyD (Mon Mar 31 2008 - 03:31:39 PDT)
- Marta Rossini (Mon Mar 31 2008 - 02:28:31 PDT)
AMBER: setBox command
- Thomas Steinbrecher (Thu Mar 06 2008 - 10:06:32 PST)
- Vijay Manickam Achari (Wed Mar 05 2008 - 21:20:01 PST)
AMBER: SMD using amber
- ChengZhong Zhang (Mon Mar 10 2008 - 18:54:23 PDT)
AMBER: solvate with methanol
- Rita Cassia (Tue Mar 11 2008 - 05:33:46 PDT)
- san_amber roy (Tue Mar 11 2008 - 02:23:40 PDT)
AMBER: SPARC benchmarks (was re Fujitsu PRIMEPOWER)
- Atro Tossavainen (Tue Mar 11 2008 - 07:33:33 PDT)
AMBER: standard residues
- Holly Freedman (Sat Mar 22 2008 - 15:27:07 PDT)
- David A. Case (Sat Mar 22 2008 - 09:30:03 PDT)
- Holly Freedman (Wed Mar 19 2008 - 13:03:02 PDT)
AMBER: study of protein stability in different ion using AMBER
- David A. Case (Fri Mar 14 2008 - 22:48:13 PDT)
- Prem Prakash Pathak (Wed Mar 12 2008 - 23:20:31 PDT)
AMBER: Temperature Range For REMD
- Carlos Simmerling (Thu Mar 13 2008 - 08:26:44 PDT)
- tushar garud (Thu Mar 13 2008 - 08:20:02 PDT)
AMBER: TI: perturbation method
- Thomas Steinbrecher (Mon Mar 31 2008 - 09:32:21 PDT)
- fatima.chami.durham.ac.uk (Mon Mar 31 2008 - 01:40:40 PDT)
AMBER: Timing analysis on Ranger
- David LeBard (Sun Mar 09 2008 - 13:06:18 PDT)
AMBER: Torsion potential in GAFF / "statistic value of parm94"
- Junmei Wang (Fri Mar 14 2008 - 20:01:20 PDT)
- Alexander Metz (Fri Mar 14 2008 - 05:53:10 PDT)
AMBER: umbrella sampling for proton transfer
- Thomas Steinbrecher (Tue Mar 25 2008 - 18:11:58 PDT)
- cniu.ualberta.ca (Tue Mar 25 2008 - 17:30:33 PDT)
AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
- Chris Moth (Wed Mar 26 2008 - 15:27:35 PDT)
- Steven Winfield (Wed Mar 26 2008 - 08:22:26 PDT)
- Qi Yan (Wed Mar 26 2008 - 07:42:54 PDT)
- Da-Wei Li (Tue Mar 25 2008 - 10:08:29 PDT)
- Qi Yan (Tue Mar 25 2008 - 10:00:35 PDT)
- Andrew Borgert (Tue Mar 25 2008 - 08:11:20 PDT)
- Qi Yan (Mon Mar 24 2008 - 13:50:40 PDT)
- Da-Wei Li (Mon Mar 24 2008 - 13:12:42 PDT)
- Qi Yan (Mon Mar 24 2008 - 13:01:35 PDT)
AMBER: Water Topology
- Ross Walker (Thu Mar 20 2008 - 08:08:46 PDT)
- Ivelin Georgiev (Thu Mar 20 2008 - 06:44:51 PDT)
- Ross Walker (Wed Mar 19 2008 - 21:49:43 PDT)
- Ivelin Georgiev (Wed Mar 19 2008 - 21:12:28 PDT)
AMBER: What's making my system lose total energy?
- David A. Case (Wed Mar 19 2008 - 18:46:31 PDT)
- David Cerutti (Tue Mar 18 2008 - 11:43:42 PDT)
- David Cerutti (Mon Mar 17 2008 - 20:52:10 PDT)
- Thomas Cheatham (Mon Mar 17 2008 - 20:36:30 PDT)
- Ross Walker (Mon Mar 17 2008 - 19:54:19 PDT)
- David Cerutti (Mon Mar 17 2008 - 17:20:30 PDT)
AMBER: writing out a distance between two atoms in sander
- Vlad Cojocaru (Mon Mar 10 2008 - 10:35:58 PDT)
- Thomas Steinbrecher (Mon Mar 10 2008 - 10:17:35 PDT)
- Vlad Cojocaru (Mon Mar 10 2008 - 06:33:55 PDT)
AMBER: Writing pressure in md.out file in NVT simulation
- Sudha Mani Karra (Mon Mar 03 2008 - 12:56:13 PST)
- Vlad Cojocaru (Mon Mar 03 2008 - 11:26:50 PST)
- David A. Case (Mon Mar 03 2008 - 11:24:20 PST)
- Sudha Mani Karra (Mon Mar 03 2008 - 10:58:46 PST)
AMBER: xleap screen output
- Bill Ross (Tue Mar 04 2008 - 09:59:58 PST)
- Francesco Pietra (Tue Mar 04 2008 - 09:33:34 PST)
- Francesco Pietra (Tue Mar 04 2008 - 09:27:00 PST)
- Bill Ross (Mon Mar 03 2008 - 14:08:17 PST)
- Francesco Pietra (Mon Mar 03 2008 - 13:48:59 PST)
- David A. Case (Mon Mar 03 2008 - 13:31:17 PST)
- Francesco Pietra (Mon Mar 03 2008 - 13:02:54 PST)
AMBER: xleap screen output SOLVED
- Francesco Pietra (Tue Mar 04 2008 - 12:44:15 PST)
AMBER: XMGRACE on Linux 64 Bit
- David LeBard (Fri Mar 07 2008 - 10:53:47 PST)
- dpandit.brandeis.edu (Fri Mar 07 2008 - 10:40:19 PST)
- Ross Walker (Thu Mar 06 2008 - 18:30:44 PST)
- dpandit.brandeis.edu (Thu Mar 06 2008 - 17:50:55 PST)
- Bill Ross (Thu Mar 06 2008 - 16:12:51 PST)
- dpandit.brandeis.edu (Thu Mar 06 2008 - 15:15:00 PST)
Force Field Parameterizing
- FyD (Tue Mar 25 2008 - 12:42:03 PDT)
- David A. Case (Tue Mar 25 2008 - 08:23:34 PDT)
- Shultz, Jack (Mon Mar 24 2008 - 08:31:32 PDT)
Fwd: AMBER: lastrst problem
- san_amber roy (Wed Mar 19 2008 - 09:07:26 PDT)
- David A. Case (Tue Mar 18 2008 - 08:37:48 PDT)
- san_amber roy (Wed Mar 12 2008 - 08:19:08 PDT)
Fwd: AMBER: Negative ligand (Peroxide)
- Syed Tarique Moin (Sun Mar 09 2008 - 22:59:43 PDT)
MD run time inquiry
- Campbell, Patrick (Thu Mar 27 2008 - 06:55:28 PDT)
- Carlos Simmerling (Thu Mar 27 2008 - 06:15:09 PDT)
- Campbell, Patrick (Thu Mar 27 2008 - 05:14:16 PDT)
- Carlos Simmerling (Thu Mar 27 2008 - 03:41:02 PDT)
- Campbell, Patrick (Thu Mar 27 2008 - 03:13:00 PDT)
Request
- Ross Walker (Fri Mar 07 2008 - 12:38:25 PST)
SV: AMBER: ptraj, hbond and non-bonded contacts
- Thomas Cheatham III (Mon Mar 17 2008 - 09:51:54 PDT)
- Samuel Genheden (a03samge) (Mon Mar 17 2008 - 04:02:59 PDT)
- Vlad Cojocaru (Mon Mar 17 2008 - 04:00:41 PDT)
- Samuel Genheden (a03samge) (Mon Mar 17 2008 - 03:43:21 PDT)
SV: SV: AMBER: ptraj, hbond and non-bonded contacts
- Samuel Genheden (a03samge) (Mon Mar 17 2008 - 13:41:31 PDT)
- Samuel Genheden (a03samge) (Mon Mar 17 2008 - 05:00:52 PDT)

Amber Archive Mar 2008 by subject