Amber Archive Jul 2008: by subject

amber 10 and mpich2 (got eof on console error message from mpich2)
- Vlad Cojocaru (Thu Jul 17 2008 - 06:33:04 PDT)
AMBER Question
- Ross Walker (Sat Jul 26 2008 - 06:53:25 PDT)
AMBER:
- Carlos Simmerling (Fri Jul 04 2008 - 05:37:29 PDT)
- Boutheina Kerkeni (Fri Jul 04 2008 - 05:27:59 PDT)
- Carlos Simmerling (Fri Jul 04 2008 - 04:50:44 PDT)
- Boutheina Kerkeni (Fri Jul 04 2008 - 04:44:20 PDT)
- Carlos Simmerling (Fri Jul 04 2008 - 04:09:07 PDT)
- Boutheina Kerkeni (Fri Jul 04 2008 - 04:02:10 PDT)
- Carlos Simmerling (Fri Jul 04 2008 - 03:42:27 PDT)
- Boutheina Kerkeni (Fri Jul 04 2008 - 03:34:55 PDT)
- Anna Reymer (Tue Jul 01 2008 - 05:46:24 PDT)
- Carlos Simmerling (Tue Jul 01 2008 - 05:15:15 PDT)
- Anna Reymer (Tue Jul 01 2008 - 01:36:12 PDT)
AMBER: "radius = 0.000"
- Arturas Ziemys (Tue Jul 01 2008 - 13:19:32 PDT)
- Robert Duke (Tue Jul 01 2008 - 11:00:38 PDT)
- Thomas Steinbrecher (Tue Jul 01 2008 - 10:36:17 PDT)
- Arturas Ziemys (Tue Jul 01 2008 - 10:17:54 PDT)
- Thomas Steinbrecher (Tue Jul 01 2008 - 09:39:30 PDT)
- Robert Duke (Tue Jul 01 2008 - 09:24:10 PDT)
- Carlos Simmerling (Tue Jul 01 2008 - 09:16:38 PDT)
- Arturas Ziemys (Tue Jul 01 2008 - 09:08:45 PDT)
AMBER: # of ligands and receptors in mmpbsa
- Scott Brozell (Thu Jul 31 2008 - 19:14:50 PDT)
- Christopher Gaughan (Fri Jul 25 2008 - 07:57:03 PDT)
AMBER: 1.5ns rst file to PDB file Conversion Error
- Ross Walker (Wed Jul 23 2008 - 02:08:46 PDT)
- khuram sb (Tue Jul 22 2008 - 22:07:24 PDT)
AMBER: [amber/glycam] dealing with fucose...
- Lachele Foley (Lists) (Tue Jul 15 2008 - 07:45:19 PDT)
- Waqas Nasir (Sat Jul 12 2008 - 12:44:13 PDT)
- Lachele Foley (Lists) (Fri Jul 11 2008 - 07:19:17 PDT)
- Waqas Nasir (Fri Jul 11 2008 - 02:47:36 PDT)
- Lachele Foley (Lists) (Thu Jul 10 2008 - 10:24:41 PDT)
- Waqas Nasir (Thu Jul 10 2008 - 05:59:34 PDT)
- Lachele Foley (Lists) (Tue Jul 08 2008 - 09:08:52 PDT)
- Waqas Nasir (Tue Jul 08 2008 - 07:56:31 PDT)
AMBER: a link for Amber ff ported to Charmm
- Alan (Sat Jul 19 2008 - 22:50:22 PDT)
- Ross Walker (Sat Jul 19 2008 - 15:28:24 PDT)
- Adrian Roitberg (Sat Jul 19 2008 - 15:10:58 PDT)
- Alan (Sat Jul 19 2008 - 14:50:25 PDT)
- David A. Case (Sat Jul 19 2008 - 11:29:18 PDT)
- Alan (Sat Jul 19 2008 - 02:07:27 PDT)
AMBER: about QMMM output
- linfu (Sat Jul 05 2008 - 19:25:47 PDT)
- Ross Walker (Fri Jul 04 2008 - 12:55:10 PDT)
- linfu (Fri Jul 04 2008 - 10:09:23 PDT)
- Ross Walker (Fri Jul 04 2008 - 09:30:09 PDT)
- Gustavo Seabra (Fri Jul 04 2008 - 08:33:06 PDT)
- linfu (Thu Jul 03 2008 - 19:40:33 PDT)
AMBER: about RMSD per residue
- Ross Walker (Wed Jul 16 2008 - 09:40:42 PDT)
- Wei Huang (Wed Jul 16 2008 - 08:31:24 PDT)
- Gustavo Seabra (Wed Jul 16 2008 - 08:22:39 PDT)
- Wei Huang (Wed Jul 16 2008 - 08:08:36 PDT)
- Ross Walker (Wed Jul 16 2008 - 07:52:38 PDT)
- Wei Huang (Wed Jul 16 2008 - 07:20:03 PDT)
- luzhenw1.msu.edu (Wed Jul 16 2008 - 06:48:05 PDT)
AMBER: ACPYPI announcement
- Alan (Thu Jul 31 2008 - 04:17:02 PDT)
AMBER: adding missing residues
- David A. Case (Thu Jul 24 2008 - 08:37:36 PDT)
- Ross Walker (Thu Jul 24 2008 - 05:35:41 PDT)
- soumick (Thu Jul 24 2008 - 04:09:16 PDT)
AMBER: Alanine scanning
- Khaled Barakat (Sun Jul 13 2008 - 18:50:47 PDT)
AMBER: amb2gmx for big systems
- rebeca.mmb.pcb.ub.es (Thu Jul 31 2008 - 03:40:39 PDT)
AMBER: amber 10 and mpich2 (got eof on console error message from mpich2)
- Vlad Cojocaru (Thu Jul 17 2008 - 06:30:24 PDT)
AMBER: Amber 10 on the BlueGene
- Carlos Simmerling (Mon Jul 28 2008 - 11:37:59 PDT)
- Robert Duke (Mon Jul 28 2008 - 10:17:18 PDT)
- Mike Hanby (Mon Jul 28 2008 - 09:15:58 PDT)
AMBER: AMBER 10: Fortran Runtime Error
- George Tzotzos (Fri Jul 25 2008 - 07:38:32 PDT)
AMBER: amber 10: sander and pmemd performance
- Robert Duke (Fri Jul 25 2008 - 09:06:41 PDT)
- Vlad Cojocaru (Fri Jul 25 2008 - 08:14:08 PDT)
- Robert Duke (Fri Jul 25 2008 - 07:31:30 PDT)
- Vlad Cojocaru (Fri Jul 25 2008 - 02:57:45 PDT)
AMBER: amber ff and how it deals with out-plane chiral C
- Bill Ross (Tue Jul 22 2008 - 14:44:36 PDT)
- Carlos Simmerling (Tue Jul 22 2008 - 08:15:56 PDT)
- Alan (Tue Jul 22 2008 - 07:41:27 PDT)
- Carlos Simmerling (Tue Jul 22 2008 - 04:57:04 PDT)
- Alan (Tue Jul 22 2008 - 00:59:05 PDT)
AMBER: Amber tools 1.2 test failure (installation)
- Myunggi Yi (Thu Jul 24 2008 - 10:09:11 PDT)
- David A. Case (Mon Jul 21 2008 - 16:36:16 PDT)
- Myunggi Yi (Mon Jul 21 2008 - 15:17:05 PDT)
AMBER: AMBER10: ambpdb problems
- Anna Reymer (Tue Jul 01 2008 - 01:37:38 PDT)
AMBER: AMBER10: Fortran Runtime Error
- Ross Walker (Fri Jul 25 2008 - 14:22:16 PDT)
- George Tzotzos (Fri Jul 25 2008 - 08:19:03 PDT)
AMBER: amber10: pmemd gfortran
- Scott Brozell (Thu Jul 31 2008 - 20:16:45 PDT)
- James W. Caldwell (Fri Jul 25 2008 - 15:06:01 PDT)
- David A. Case (Fri Jul 25 2008 - 12:05:23 PDT)
- Robert Duke (Fri Jul 25 2008 - 12:01:27 PDT)
- James W. Caldwell (Fri Jul 25 2008 - 11:23:06 PDT)
AMBER: amber9 / difference of igb=0 and igb=6
- Arturas Ziemys (Wed Jul 09 2008 - 14:03:32 PDT)
- Ross Walker (Wed Jul 09 2008 - 13:54:54 PDT)
- Arturas Ziemys (Wed Jul 09 2008 - 12:45:32 PDT)
AMBER: amber9 install problem
- David A. Case (Thu Jul 24 2008 - 08:08:21 PDT)
- hklwatergod (Wed Jul 23 2008 - 23:11:33 PDT)
AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj?
- Hannes Loeffler (Wed Jul 23 2008 - 04:11:57 PDT)
- Thomas Cheatham (Tue Jul 22 2008 - 09:45:12 PDT)
- Hannes Loeffler (Tue Jul 22 2008 - 07:08:36 PDT)
AMBER: AmberTools-1.1 port for FreeBSD
- M. L. Dodson (Thu Jul 17 2008 - 10:59:05 PDT)
AMBER: AmberTools1.1 (and 1.0) antechamber endless loop
- Ross Walker (Tue Jul 15 2008 - 09:01:55 PDT)
- Ross Walker (Tue Jul 15 2008 - 08:50:20 PDT)
- Grange Hermitage (Mon Jul 14 2008 - 17:18:40 PDT)
- Grange Hermitage (Mon Jul 14 2008 - 00:41:40 PDT)
- Ross Walker (Sun Jul 13 2008 - 21:35:42 PDT)
- Grange Hermitage (Sun Jul 13 2008 - 18:06:33 PDT)
AMBER: analysing normal modes
- Vahdati N. (Thu Jul 10 2008 - 05:49:15 PDT)
- Chris Moth (Wed Jul 09 2008 - 12:45:57 PDT)
- Vahdati N. (Tue Jul 08 2008 - 11:03:39 PDT)
AMBER: antechamber and charmm
- David A. Case (Thu Jul 17 2008 - 09:16:02 PDT)
- Alan (Thu Jul 17 2008 - 09:05:40 PDT)
- Junmei Wang (Thu Jul 17 2008 - 07:33:23 PDT)
- Alan (Thu Jul 10 2008 - 02:43:58 PDT)
AMBER: antechamber generated input for gaussian error
- Junmei Wang (Wed Jul 23 2008 - 08:29:21 PDT)
- Grange Hermitage (Sat Jul 19 2008 - 17:53:49 PDT)
AMBER: Atom type with 10-12 and 6-12 interactions in Amber9
- Brad Lambeth (Sat Jul 12 2008 - 17:20:09 PDT)
AMBER: bad nonbon in nmode (amber9)
- Enghui Yap (Mon Jul 14 2008 - 09:25:29 PDT)
AMBER: bellymask for DNA backbone doesn't seem to work
- Thomas Cheatham III (Thu Jul 03 2008 - 13:40:47 PDT)
- Seth Lilavivat (Thu Jul 03 2008 - 13:13:40 PDT)
AMBER: big molecule numbers
- Ross Walker (Fri Jul 25 2008 - 01:10:05 PDT)
- David A. Case (Thu Jul 24 2008 - 18:43:26 PDT)
- Adrien Delmont (Thu Jul 24 2008 - 15:27:22 PDT)
AMBER: big molecule numbers ( simulation with many formamide molecules )
- Ross Walker (Sun Jul 27 2008 - 02:19:41 PDT)
- Adrien Delmont (Sat Jul 26 2008 - 08:55:11 PDT)
- Ross Walker (Sat Jul 26 2008 - 06:58:34 PDT)
- Adrien Delmont (Sat Jul 26 2008 - 02:04:08 PDT)
AMBER: bond command
- Boutheina Kerkeni (Fri Jul 11 2008 - 05:00:48 PDT)
- Ross Walker (Thu Jul 10 2008 - 12:15:53 PDT)
- M. L. Dodson (Thu Jul 10 2008 - 11:34:33 PDT)
- Wang,Ying (Thu Jul 10 2008 - 10:56:01 PDT)
- Boutheina Kerkeni (Thu Jul 10 2008 - 10:30:46 PDT)
AMBER: calculating the enthalpy of evaporation
- David A. Case (Thu Jul 24 2008 - 13:31:01 PDT)
- jessica stolee (Thu Jul 24 2008 - 12:24:40 PDT)
AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP
- Bill Ross (Mon Jul 28 2008 - 17:26:35 PDT)
- Sandeep Kaushik (Mon Jul 28 2008 - 05:30:16 PDT)
- Bill Ross (Fri Jul 25 2008 - 13:40:27 PDT)
- Lachele Foley (Lists) (Fri Jul 25 2008 - 07:47:54 PDT)
- Sandeep Kaushik (Fri Jul 25 2008 - 03:04:11 PDT)
AMBER: compile amber10 on Mac
- Scott Brozell (Thu Jul 03 2008 - 18:38:19 PDT)
- Junmei Wang (Tue Jul 01 2008 - 14:45:31 PDT)
AMBER: concerning force fields ( to Karl Kirschner )
- Karl Kirschner (kkirschn) (Tue Jul 01 2008 - 08:06:29 PDT)
- Adrien Delmont (Tue Jul 01 2008 - 01:04:45 PDT)
AMBER: configure_amber (10) for pg compilers
- Robert Duke (Fri Jul 11 2008 - 05:27:02 PDT)
- Vlad Cojocaru (Fri Jul 11 2008 - 04:51:47 PDT)
AMBER: Constant pH with new parameters (amber10)
- Markus Kaukonen (Sun Jul 20 2008 - 01:08:35 PDT)
- Adrian Roitberg (Sat Jul 12 2008 - 16:47:41 PDT)
- Markus Kaukonen (Sat Jul 12 2008 - 12:24:05 PDT)
- David A. Case (Fri Jul 11 2008 - 11:41:09 PDT)
- Markus Kaukonen (Tue Jul 08 2008 - 00:39:57 PDT)
AMBER: difference between sander and NAB
- Hu, Shaowen (JSC-SK)[USRA] (Fri Jul 11 2008 - 06:02:51 PDT)
- David A. Case (Thu Jul 10 2008 - 15:22:49 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Thu Jul 10 2008 - 12:44:41 PDT)
AMBER: Distance diagnolization matrix plot
- Siddharth Rastogi (Wed Jul 09 2008 - 00:04:08 PDT)
AMBER: DMSOBOX
- Panwang Zhou (Wed Jul 30 2008 - 00:31:53 PDT)
- jacopo.sgrignani.unifi.it (Wed Jul 30 2008 - 00:05:00 PDT)
AMBER: Does clustering involve fitting?
- Jianyin Shao (Wed Jul 30 2008 - 14:29:57 PDT)
- Steve Spronk (Fri Jul 25 2008 - 13:02:09 PDT)
AMBER: empty output
- Boutheina Kerkeni (Tue Jul 15 2008 - 10:31:50 PDT)
- Ross Walker (Sat Jul 12 2008 - 09:54:01 PDT)
- Boutheina Kerkeni (Sat Jul 12 2008 - 08:29:47 PDT)
AMBER: Energy analysis
- aneesh cna (Fri Jul 25 2008 - 08:12:10 PDT)
AMBER: Energy minimization of protein-ligand complex
- Dong Xu (Tue Jul 29 2008 - 00:18:57 PDT)
AMBER: Error when performing Alanine scanning
- Khaled Barakat (Mon Jul 14 2008 - 18:41:26 PDT)
AMBER: EVB tests failure
- Vlad Cojocaru (Thu Jul 24 2008 - 01:34:52 PDT)
AMBER: files in Amber directory ( to Junmei Wang )
- John Bennett (Fri Jul 18 2008 - 04:25:38 PDT)
- Junmei Wang (Thu Jul 17 2008 - 07:56:06 PDT)
- David A. Case (Tue Jul 15 2008 - 11:55:41 PDT)
- John Bennett (Tue Jul 15 2008 - 04:10:40 PDT)
AMBER: For help: how to perform double decoupling thermodynamic integration calculation in AMBER10
- Thomas Steinbrecher (Mon Jul 07 2008 - 15:56:49 PDT)
- yongleli (Mon Jul 07 2008 - 15:04:53 PDT)
AMBER: For help: Thermodynamic Integration of solvation free energy using soft-core potential
- Thomas Steinbrecher (Wed Jul 02 2008 - 12:08:40 PDT)
- yongleli (Wed Jul 02 2008 - 11:19:03 PDT)
AMBER: for mask in rms
- Wenyong Tong (Tue Jul 29 2008 - 20:35:23 PDT)
AMBER: Force Field parameters : A new chemical compound
- Chih-Ying Lin (Thu Jul 03 2008 - 10:52:17 PDT)
AMBER: Force fields for REMD with GB solvent
- Carlos Simmerling (Wed Jul 09 2008 - 06:37:36 PDT)
- guardiani.fi.infn.it (Wed Jul 09 2008 - 02:37:43 PDT)
- Carlos Simmerling (Tue Jul 08 2008 - 15:03:31 PDT)
- guardiani.fi.infn.it (Tue Jul 08 2008 - 09:24:27 PDT)
AMBER: fortran runtime error in "make test.serial" with gfortran
- David A. Case (Fri Jul 25 2008 - 16:03:57 PDT)
- Jaber Jahanbin Sardroodi (Fri Jul 25 2008 - 15:23:25 PDT)
AMBER: free energy
- Boutheina Kerkeni (Wed Jul 16 2008 - 09:30:44 PDT)
- Thomas Steinbrecher (Wed Jul 16 2008 - 09:22:45 PDT)
- Adrian Roitberg (Wed Jul 16 2008 - 07:10:41 PDT)
- Christopher Gaughan (Wed Jul 16 2008 - 09:03:26 PDT)
- Boutheina Kerkeni (Wed Jul 16 2008 - 08:54:39 PDT)
AMBER: FreeBSD "port" for AmberTools-1.2
- M. L. Dodson (Tue Jul 22 2008 - 12:30:27 PDT)
- M. L. Dodson (Tue Jul 22 2008 - 12:15:48 PDT)
AMBER: High force constant for MD ???
- Waqas Nasir (Thu Jul 24 2008 - 03:42:13 PDT)
- Carlos Simmerling (Wed Jul 23 2008 - 04:02:13 PDT)
- Waqas Nasir (Wed Jul 23 2008 - 02:49:46 PDT)
AMBER: how to generate psf file using the AMBER topology file
- tinni sona (Sat Jul 19 2008 - 22:38:10 PDT)
- Ross Walker (Fri Jul 18 2008 - 09:57:14 PDT)
- tinni sona (Fri Jul 18 2008 - 05:08:48 PDT)
- Balazs JOJART (Fri Jul 18 2008 - 04:09:21 PDT)
- tinni sona (Fri Jul 18 2008 - 03:41:11 PDT)
AMBER: how to get the potential energy of a protein from the system
- David A. Case (Thu Jul 31 2008 - 07:45:47 PDT)
- TaoPaul (Thu Jul 31 2008 - 01:29:08 PDT)
AMBER: How to obtain the oriented trajectories?
- Carlos Simmerling (Thu Jul 03 2008 - 07:22:03 PDT)
- Panwang Zhou (Thu Jul 03 2008 - 07:06:58 PDT)
AMBER: Hydroxyproline in AMBER
- Adrian Roitberg (Wed Jul 23 2008 - 09:14:06 PDT)
- Carlos Simmerling (Wed Jul 23 2008 - 09:03:01 PDT)
- Michael Entz (Wed Jul 23 2008 - 08:40:05 PDT)
AMBER: imin = 5 and PBC
- sai kumar ramadugu (Thu Jul 31 2008 - 07:51:21 PDT)
AMBER: improper dihedral in ff03 united atom forcefield
- Bill Ross (Wed Jul 23 2008 - 11:19:31 PDT)
- 秦姗姗 (Tue Jul 22 2008 - 22:14:11 PDT)
- Bill Ross (Tue Jul 22 2008 - 21:28:07 PDT)
- 秦姗姗 (Tue Jul 22 2008 - 18:49:28 PDT)
AMBER: improper dihedrals in 03 united atom force field
- Q733 (Tue Jul 22 2008 - 19:00:03 PDT)
AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ?
- Robert Duke (Wed Jul 02 2008 - 17:06:22 PDT)
- Robert Duke (Wed Jul 02 2008 - 17:00:07 PDT)
- David A. Case (Wed Jul 02 2008 - 15:58:36 PDT)
- Arturas Ziemys (Wed Jul 02 2008 - 15:48:47 PDT)
- Robert Duke (Wed Jul 02 2008 - 15:36:12 PDT)
- Ross Walker (Wed Jul 02 2008 - 15:30:21 PDT)
- Robert Duke (Wed Jul 02 2008 - 15:29:52 PDT)
- Robert Duke (Wed Jul 02 2008 - 15:28:10 PDT)
- David A. Case (Wed Jul 02 2008 - 15:25:18 PDT)
- Arturas Ziemys (Wed Jul 02 2008 - 15:10:47 PDT)
AMBER: Indentifying cluster center structures in trajectory
- Ross Walker (Wed Jul 23 2008 - 02:14:27 PDT)
- Anselm Horn (Wed Jul 23 2008 - 00:14:41 PDT)
AMBER: Installation of Amber 10 on Dual-Core Intel Mac
- George Tzotzos (Fri Jul 11 2008 - 13:33:55 PDT)
AMBER: Installation on Mac OSX G5 dual processor
- George Tzotzos (Fri Jul 11 2008 - 13:30:21 PDT)
AMBER: interaction energies in Amber
- Alessandro Nascimento (Mon Jul 28 2008 - 17:51:01 PDT)
AMBER: interaction energies in Amber and VMD/NAMD
- Alan (Tue Jul 29 2008 - 03:10:48 PDT)
- Alan (Tue Jul 29 2008 - 01:19:16 PDT)
- Alessandro Nascimento (Sun Jul 27 2008 - 17:38:56 PDT)
- Alan (Sat Jul 26 2008 - 23:26:32 PDT)
- Carlos Simmerling (Sat Jul 26 2008 - 17:46:58 PDT)
- David A. Case (Sat Jul 26 2008 - 17:36:46 PDT)
- Carlos Simmerling (Sat Jul 26 2008 - 10:20:11 PDT)
- Alessandro Nascimento (Sat Jul 26 2008 - 09:09:38 PDT)
AMBER: interaction energies in Amber and VMD/NAMD (SOLVED)
- Alessandro Nascimento (Wed Jul 30 2008 - 08:29:47 PDT)
AMBER: is amber workshop available this summer??
- Ross Walker (Wed Jul 02 2008 - 21:19:31 PDT)
- Chih-Ying Lin (Wed Jul 02 2008 - 16:29:03 PDT)
AMBER: Ligand force field generation, and its consistency with the force field of the protein.
- SeungPyo Hong (Wed Jul 16 2008 - 18:50:31 PDT)
- Gustavo Seabra (Wed Jul 16 2008 - 07:08:45 PDT)
- Alan (Wed Jul 16 2008 - 05:46:15 PDT)
- SeungPyo Hong (Wed Jul 16 2008 - 05:15:48 PDT)
AMBER: mask for oligosaccharide
- Wenyong Tong (Wed Jul 30 2008 - 21:13:08 PDT)
- Jianyin Shao (Wed Jul 30 2008 - 15:26:31 PDT)
- Wenyong Tong (Wed Jul 30 2008 - 11:23:58 PDT)
AMBER: mm_pbsa incorrect complex prmtop file
- Neha Gandhi (Thu Jul 10 2008 - 01:02:27 PDT)
- xiaonan zhang (Thu Jul 10 2008 - 00:44:58 PDT)
AMBER: Model of deoxyadenosine in Cornell 95 paper
- Piotr Cieplak (Tue Jul 15 2008 - 23:32:08 PDT)
- Ilyas Yildirim (Sun Jul 13 2008 - 16:14:48 PDT)
AMBER: NMA
- David A. Case (Fri Jul 11 2008 - 11:19:06 PDT)
- Steve Seibold (Fri Jul 11 2008 - 09:34:00 PDT)
AMBER: Nmode entropy calcs
- David A. Case (Sun Jul 13 2008 - 08:45:56 PDT)
- Sergio Wong (Sat Jul 12 2008 - 18:09:51 PDT)
AMBER: NMR refinement
- teresa.ierano.unina.it (Thu Jul 03 2008 - 02:37:02 PDT)
- David A. Case (Wed Jul 02 2008 - 17:21:54 PDT)
- Ilyas Yildirim (Wed Jul 02 2008 - 02:58:05 PDT)
- teresa.ierano.unina.it (Wed Jul 02 2008 - 01:38:57 PDT)
AMBER: NONBONDED_PARM_INDEX
- David A. Case (Wed Jul 02 2008 - 08:04:26 PDT)
- Max (Wed Jul 02 2008 - 01:54:35 PDT)
AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why?
- Alan (Mon Jul 28 2008 - 07:50:00 PDT)
- Carlos Simmerling (Mon Jul 28 2008 - 06:52:08 PDT)
- Alan (Mon Jul 28 2008 - 06:21:35 PDT)
- Carlos Simmerling (Mon Jul 28 2008 - 05:54:51 PDT)
- FyD (Mon Jul 28 2008 - 05:28:50 PDT)
- Alan (Mon Jul 28 2008 - 03:54:31 PDT)
- Alan (Sat Jul 26 2008 - 01:33:46 PDT)
AMBER: opls/aa in Amber status
- Alan (Thu Jul 31 2008 - 01:41:58 PDT)
AMBER: parameters for Fe coordinated to four CYS ?
- Jose Borreguero (Tue Jul 01 2008 - 17:12:37 PDT)
AMBER: paricular atom coordinates?
- Vijay Singh (Thu Jul 17 2008 - 09:13:30 PDT)
AMBER: parmbsc0
- Dr. Suzie Byun (Sat Jul 19 2008 - 08:40:05 PDT)
AMBER: pmemd 10 output
- Vlad Cojocaru (Thu Jul 10 2008 - 07:18:28 PDT)
- Robert Duke (Thu Jul 10 2008 - 06:44:19 PDT)
- Vlad Cojocaru (Thu Jul 10 2008 - 06:29:17 PDT)
- Vlad Cojocaru (Thu Jul 10 2008 - 06:26:01 PDT)
- Robert Duke (Thu Jul 10 2008 - 06:12:25 PDT)
- Vlad Cojocaru (Thu Jul 10 2008 - 03:19:08 PDT)
AMBER: PMEMD and polarized force field ff 02
- Abhishek Singh (Thu Jul 03 2008 - 07:53:36 PDT)
- David A. Case (Thu Jul 03 2008 - 08:10:06 PDT)
- Ross Walker (Thu Jul 03 2008 - 08:02:17 PDT)
- Abhishek Singh (Thu Jul 03 2008 - 07:50:00 PDT)
AMBER: PMEND 9 compilation problems
- Robert Duke (Wed Jul 30 2008 - 07:40:00 PDT)
- Nick Holway (Wed Jul 30 2008 - 06:50:42 PDT)
- Robert Duke (Tue Jul 29 2008 - 10:41:54 PDT)
- Nick Holway (Tue Jul 29 2008 - 09:04:36 PDT)
AMBER: POL3 with gaff and ff02EP
- Ross Walker (Sun Jul 13 2008 - 21:40:02 PDT)
- Grange Hermitage (Sun Jul 13 2008 - 18:15:43 PDT)
AMBER: Polarizable force field for divalent ions?
- Yi-Ming Cheng (Wed Jul 23 2008 - 03:59:08 PDT)
AMBER: prepare an initial structure in Amber
- oguz gurbulak (Thu Jul 31 2008 - 09:58:24 PDT)
AMBER: Prepgen
- Heikki Salo (Wed Jul 30 2008 - 01:58:28 PDT)
AMBER: Problem in .parmtop file
- sudipta sinha (Mon Jul 28 2008 - 08:30:09 PDT)
AMBER: Problem with box dimension in AmberTools ptraj
- Thomas Cheatham (Tue Jul 22 2008 - 09:47:42 PDT)
- Steve Spronk (Mon Jul 21 2008 - 23:35:47 PDT)
AMBER: problem with rdparm
- Thomas Cheatham III (Thu Jul 10 2008 - 15:13:35 PDT)
- Harry (Yicun) Ni (Thu Jul 10 2008 - 15:05:41 PDT)
AMBER: problem with restraints
- Barbault Florent (Thu Jul 10 2008 - 11:59:15 PDT)
AMBER: Problems in restrained minimization
- julliane Yoneda (Wed Jul 23 2008 - 06:08:32 PDT)
AMBER: Problems with Frozen atoms
- julliane Yoneda (Fri Jul 18 2008 - 13:06:54 PDT)
AMBER: protonated guanine, cytosine parameters
- Kliman, Michal (Tue Jul 22 2008 - 15:22:19 PDT)
AMBER: Protonated Phosphate Problem
- Thomas Steinbrecher (Tue Jul 01 2008 - 10:41:55 PDT)
- Kliman, Michal (Tue Jul 01 2008 - 10:20:14 PDT)
AMBER: ptraj problem with centering in the box
- Ross Walker (Wed Jul 02 2008 - 08:31:51 PDT)
- Hannes Wallnoefer (Wed Jul 02 2008 - 07:00:33 PDT)
AMBER: ptraj problem with imaging
- fatima.chami.durham.ac.uk (Thu Jul 03 2008 - 09:11:19 PDT)
- Ross Walker (Wed Jul 02 2008 - 13:06:42 PDT)
- fatima.chami.durham.ac.uk (Wed Jul 02 2008 - 09:52:32 PDT)
AMBER: ptraj selection
- Ilyas Yildirim (Thu Jul 10 2008 - 17:58:08 PDT)
- Jianyin Shao (Thu Jul 10 2008 - 08:56:55 PDT)
- David Watson (Wed Jul 09 2008 - 23:01:01 PDT)
- Ilyas Yildirim (Wed Jul 09 2008 - 21:27:35 PDT)
- David Watson (Wed Jul 09 2008 - 20:59:27 PDT)
- Ilyas Yildirim (Wed Jul 09 2008 - 20:13:22 PDT)
- David Watson (Wed Jul 09 2008 - 19:11:16 PDT)
- Ilyas Yildirim (Wed Jul 09 2008 - 18:07:39 PDT)
AMBER: ptraj: projection command missing in dispatch.c (AMBER 10)
- David A. Case (Tue Jul 15 2008 - 11:57:52 PDT)
- Vlad Cojocaru (Tue Jul 15 2008 - 06:45:11 PDT)
AMBER: Q: ntc = 3 parallel runnable not compiled in Amber 9?
- Carlos Simmerling (Thu Jul 31 2008 - 05:07:21 PDT)
- Qicun Shi (Wed Jul 30 2008 - 20:51:17 PDT)
AMBER: querry
- Lachele Foley (Lists) (Tue Jul 22 2008 - 06:55:08 PDT)
- Sandeep Kaushik (Tue Jul 22 2008 - 05:09:08 PDT)
- dipti lele (Mon Jul 14 2008 - 01:05:15 PDT)
AMBER: Query
- Ross Walker (Sun Jul 27 2008 - 02:04:57 PDT)
- dipti lele (Sat Jul 26 2008 - 23:40:54 PDT)
AMBER: Query about the charge of atoms in the parmtop file
- Alan (Fri Jul 25 2008 - 12:13:43 PDT)
- Carlos Simmerling (Thu Jul 24 2008 - 06:09:45 PDT)
- Ross Walker (Thu Jul 24 2008 - 05:49:03 PDT)
- tinni sona (Thu Jul 24 2008 - 00:19:26 PDT)
- Carlos Simmerling (Wed Jul 23 2008 - 10:16:09 PDT)
- tinni sona (Wed Jul 23 2008 - 09:48:19 PDT)
AMBER: Question about loading frcmod.ionsjc_tip3p in xleap
- Scott Brozell (Thu Jul 31 2008 - 15:40:43 PDT)
- Jeff Schwinefus (Fri Jul 11 2008 - 09:41:21 PDT)
- David A. Case (Thu Jul 10 2008 - 21:42:28 PDT)
- Thomas Cheatham III (Thu Jul 10 2008 - 15:20:04 PDT)
- Jeff Schwinefus (Wed Jul 09 2008 - 14:27:46 PDT)
AMBER: question about the improper torsion
- Bill Ross (Tue Jul 15 2008 - 09:48:24 PDT)
- Harry (Yicun) Ni (Mon Jul 14 2008 - 21:12:57 PDT)
- David A. Case (Sat Jul 12 2008 - 07:43:46 PDT)
- Harry (Yicun) Ni (Fri Jul 11 2008 - 09:34:17 PDT)
AMBER: radius of calcium ion in MM_PBSA
- Navnit Kumar Mishra (Mon Jul 28 2008 - 02:55:33 PDT)
- Hannes Wallnoefer (Mon Jul 28 2008 - 02:28:01 PDT)
- Neha Gandhi (Mon Jul 28 2008 - 01:46:50 PDT)
- Hannes Wallnoefer (Mon Jul 28 2008 - 01:18:22 PDT)
AMBER: RDF in ptraj
- fatima.chami.durham.ac.uk (Tue Jul 01 2008 - 06:34:35 PDT)
AMBER: RED III execution problem
- FyD (Mon Jul 07 2008 - 13:54:30 PDT)
- ben rodriguez (Mon Jul 07 2008 - 12:21:11 PDT)
- FyD (Thu Jul 03 2008 - 02:25:24 PDT)
- ben rodriguez (Wed Jul 02 2008 - 18:24:19 PDT)
AMBER: Regarding ff03 forcefield
- David A. Case (Fri Jul 25 2008 - 13:46:26 PDT)
- Bill Ross (Fri Jul 25 2008 - 13:32:02 PDT)
- Yong Duan (Fri Jul 25 2008 - 09:24:19 PDT)
- Ross Walker (Fri Jul 25 2008 - 01:16:57 PDT)
- Reena ..... (Fri Jul 25 2008 - 00:24:41 PDT)
AMBER: Regarding force field ff02 and ion library
- Abhishek Singh (Tue Jul 01 2008 - 12:02:28 PDT)
AMBER: Release of version 1.2 of AmberTools
- David A. Case (Mon Jul 21 2008 - 10:01:29 PDT)
AMBER: REMD temperature profile
- Carlos Simmerling (Wed Jul 09 2008 - 08:28:59 PDT)
- guardiani.fi.infn.it (Wed Jul 09 2008 - 06:47:13 PDT)
AMBER: replicas trapped in a few low temperatures
- Carlos Simmerling (Thu Jul 10 2008 - 06:11:33 PDT)
- Ye Mei (Thu Jul 10 2008 - 05:35:41 PDT)
- Carlos Simmerling (Thu Jul 10 2008 - 05:12:51 PDT)
- Ye Mei (Thu Jul 10 2008 - 05:11:28 PDT)
- Carlos Simmerling (Thu Jul 10 2008 - 05:00:58 PDT)
- Ye Mei (Thu Jul 10 2008 - 04:49:08 PDT)
- Carlos Simmerling (Thu Jul 10 2008 - 04:23:39 PDT)
- Ye Mei (Thu Jul 10 2008 - 04:16:59 PDT)
- Carlos Simmerling (Thu Jul 10 2008 - 03:59:03 PDT)
- Ye Mei (Thu Jul 10 2008 - 02:13:25 PDT)
AMBER: Res minimization
- gurpreet singh (Tue Jul 15 2008 - 21:25:54 PDT)
- Ross Walker (Tue Jul 15 2008 - 08:53:46 PDT)
- Thomas Leonard (Tue Jul 15 2008 - 00:34:47 PDT)
AMBER: RESP calculation on Copper containing molecule
- FyD (Fri Jul 04 2008 - 03:25:42 PDT)
- Vidana.Epa.csiro.au (Fri Jul 04 2008 - 00:16:24 PDT)
AMBER: Restarting Problem in MD Simulation
- Ross Walker (Fri Jul 18 2008 - 10:08:46 PDT)
- khuram sb (Fri Jul 18 2008 - 03:37:07 PDT)
AMBER: RMSD per residue
- gurpreet singh (Tue Jul 15 2008 - 21:13:59 PDT)
- luzhenw1.msu.edu (Tue Jul 15 2008 - 13:28:08 PDT)
AMBER: Running patch "bugfix.at.all" with AmberTools 1.2
- Scott Brozell (Thu Jul 31 2008 - 15:04:55 PDT)
- Mike Hanby (Fri Jul 25 2008 - 09:16:37 PDT)
- David A. Case (Thu Jul 24 2008 - 16:37:32 PDT)
- Mike Hanby (Thu Jul 24 2008 - 14:47:34 PDT)
AMBER: SCC-DFTB for Zinc atom
- Gustavo Seabra (Fri Jul 18 2008 - 16:21:45 PDT)
- Jifeng Wang (Fri Jul 18 2008 - 10:10:17 PDT)
- Gustavo Seabra (Thu Jul 17 2008 - 08:48:33 PDT)
- Jifeng Wang (Thu Jul 17 2008 - 08:33:15 PDT)
AMBER: SHIFTS compile error
- David A. Case (Wed Jul 23 2008 - 10:22:32 PDT)
- IN SUK JOUNG (Tue Jul 22 2008 - 13:25:43 PDT)
AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
- Dong Xu (Tue Jul 29 2008 - 00:40:04 PDT)
- Jianyin Shao (Tue Jul 08 2008 - 21:45:46 PDT)
- Dong Xu (Mon Jul 07 2008 - 23:37:54 PDT)
- Jianyin Shao (Mon Jul 07 2008 - 15:41:03 PDT)
- Dong Xu (Fri Jul 04 2008 - 12:21:31 PDT)
- Dong Xu (Thu Jul 03 2008 - 23:33:03 PDT)
- Dong Xu (Thu Jul 03 2008 - 23:28:44 PDT)
AMBER: simulation with many formamide molecules
- Adrien Delmont (Fri Jul 25 2008 - 03:44:23 PDT)
AMBER: size of pdb
- David A. Case (Sat Jul 12 2008 - 07:45:51 PDT)
- Boutheina Kerkeni (Fri Jul 11 2008 - 08:13:57 PDT)
AMBER: sleap test failures
- Vlad Cojocaru (Wed Jul 16 2008 - 05:40:12 PDT)
- Vlad Cojocaru (Wed Jul 16 2008 - 01:07:48 PDT)
- David A. Case (Tue Jul 15 2008 - 15:46:00 PDT)
- Vlad Cojocaru (Tue Jul 15 2008 - 07:14:23 PDT)
AMBER: solvate dna in TIP3PBOX 10.0
- Bill Ross (Sat Jul 26 2008 - 11:11:44 PDT)
- Collins Nganou (Sat Jul 26 2008 - 02:08:26 PDT)
- Bill Ross (Fri Jul 25 2008 - 13:28:46 PDT)
- Ross Walker (Fri Jul 25 2008 - 01:14:26 PDT)
- Collins Nganou (Thu Jul 24 2008 - 23:51:54 PDT)
- Ross Walker (Thu Jul 24 2008 - 05:29:51 PDT)
- Collins Nganou (Thu Jul 24 2008 - 02:28:44 PDT)
AMBER: targeted MD
- Carlos Simmerling (Tue Jul 22 2008 - 04:48:15 PDT)
- Germain Vallverdu (Tue Jul 22 2008 - 03:08:04 PDT)
AMBER: test of parallel sander 10 fail
- Thomas Cheatham III (Tue Jul 15 2008 - 10:41:12 PDT)
- Vlad Cojocaru (Tue Jul 15 2008 - 10:05:51 PDT)
AMBER: the install problem
- hklwatergod (Mon Jul 28 2008 - 07:22:58 PDT)
- Ross Walker (Sun Jul 27 2008 - 02:00:59 PDT)
- hklwatergod (Sat Jul 26 2008 - 23:34:55 PDT)
AMBER: The list-directed or NAMELIST READ statement cannot be completed
- Ross Walker (Thu Jul 17 2008 - 09:55:22 PDT)
- Carlos Simmerling (Thu Jul 17 2008 - 09:47:24 PDT)
- rebeca (Thu Jul 17 2008 - 09:42:25 PDT)
AMBER: the plot of the groove width versus time for RNA
- 欧阳德方 (Thu Jul 17 2008 - 16:35:31 PDT)
AMBER: the pmemd problem
- Robert Duke (Fri Jul 25 2008 - 06:46:24 PDT)
- hklwatergod (Fri Jul 25 2008 - 04:51:32 PDT)
AMBER: timing info output from pmemd
- Vlad Cojocaru (Fri Jul 11 2008 - 06:54:02 PDT)
- Robert Duke (Fri Jul 11 2008 - 06:41:21 PDT)
- Vlad Cojocaru (Fri Jul 11 2008 - 05:33:31 PDT)
- Robert Duke (Fri Jul 11 2008 - 05:14:29 PDT)
- Vlad Cojocaru (Fri Jul 11 2008 - 01:49:28 PDT)
AMBER: Trans proline
- dipti lele (Wed Jul 23 2008 - 04:01:28 PDT)
- Adrian Roitberg (Sun Jul 20 2008 - 05:27:45 PDT)
- Carlos Simmerling (Sun Jul 20 2008 - 04:50:39 PDT)
- Barbault Florent (Sat Jul 19 2008 - 23:27:37 PDT)
- dipti lele (Sat Jul 19 2008 - 22:53:00 PDT)
AMBER: trouble interpreting <P2> time correlation function data
- Sally Pias (Sun Jul 06 2008 - 10:08:18 PDT)
- David A. Case (Sun Jul 06 2008 - 08:04:30 PDT)
- Sally Pias (Sat Jul 05 2008 - 23:59:57 PDT)
AMBER: Tutorial 6
- Ross Walker (Mon Jul 14 2008 - 11:48:05 PDT)
- Beale, John (Mon Jul 14 2008 - 09:48:21 PDT)
AMBER: Volume of ucell too big
- David A. Case (Tue Jul 29 2008 - 22:19:31 PDT)
- baohua zhang (Tue Jul 29 2008 - 20:30:43 PDT)
AMBER: Where is ICO read from the ix array?
- David A. Case (Mon Jul 21 2008 - 16:54:18 PDT)
- Brad Lambeth (Mon Jul 21 2008 - 12:49:44 PDT)
AMBER: Which CO2 potential?
- Gustavo Seabra (Thu Jul 24 2008 - 06:08:53 PDT)
- Jones de Andrade (Wed Jul 23 2008 - 20:45:00 PDT)
- gustavo.seabra.gmail.com (Wed Jul 23 2008 - 20:32:58 PDT)
- Jones de Andrade (Wed Jul 23 2008 - 17:27:58 PDT)
AMBER: XLeap Problems
- Ross Walker (Wed Jul 09 2008 - 11:08:50 PDT)
- Mark Williamson (Wed Jul 09 2008 - 09:41:51 PDT)
- Schwehm, Jeffrey M. (Wed Jul 09 2008 - 09:26:14 PDT)
AMBER:Some questions about replica exchan ge
- Carlos Simmerling (Wed Jul 16 2008 - 08:04:25 PDT)
- Ross Walker (Wed Jul 16 2008 - 07:45:38 PDT)
- huzehan19870731.126.com (Wed Jul 16 2008 - 06:07:46 PDT)
FreeBSD "port" for AmberTools-1.2
- M. L. Dodson (Wed Jul 23 2008 - 07:17:56 PDT)

Amber Archive Jul 2008 by subject