AMBER Archive (2008) - Jul 2008 By ThreadMost recent messages
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Starting: Tue Jul 01 2008 - 03:04:45 CDT
Ending: Thu Jul 31 2008 - 22:21:54 CDT
- AMBER: concerning force fields ( to Karl Kirschner ) Adrien Delmont (Tue Jul 01 2008 - 03:04:45 CDT)
- AMBER: Anna Reymer (Tue Jul 01 2008 - 03:36:12 CDT)
- AMBER: AMBER10: ambpdb problems Anna Reymer (Tue Jul 01 2008 - 03:37:38 CDT)
- AMBER: RDF in ptraj fatima.chami_at_durham.ac.uk (Tue Jul 01 2008 - 08:34:35 CDT)
- AMBER: "radius = 0.000" Arturas Ziemys (Tue Jul 01 2008 - 11:08:45 CDT)
- AMBER: Protonated Phosphate Problem Kliman, Michal (Tue Jul 01 2008 - 12:20:14 CDT)
- AMBER: compile amber10 on Mac Junmei Wang (Tue Jul 01 2008 - 16:45:31 CDT)
- AMBER: parameters for Fe coordinated to four CYS ? Jose Borreguero (Tue Jul 01 2008 - 19:12:37 CDT)
- AMBER: NMR refinement teresa.ierano_at_unina.it (Wed Jul 02 2008 - 03:38:57 CDT)
- AMBER: NONBONDED_PARM_INDEX Max (Wed Jul 02 2008 - 03:54:35 CDT)
- AMBER: ptraj problem with imaging fatima.chami_at_durham.ac.uk (Wed Jul 02 2008 - 11:52:32 CDT)
- AMBER: For help: Thermodynamic Integration of solvation free energy using soft-core potential yongleli (Wed Jul 02 2008 - 13:19:03 CDT)
- AMBER: RED III execution problem ben rodriguez (Wed Jul 02 2008 - 20:24:19 CDT)
- AMBER: How to obtain the oriented trajectories? Panwang Zhou (Thu Jul 03 2008 - 09:06:58 CDT)
- AMBER: PMEMD and polarized force field ff 02 Abhishek Singh (Thu Jul 03 2008 - 09:50:00 CDT)
- AMBER: PMEMD and polarized force field ff 02 Abhishek Singh (Thu Jul 03 2008 - 09:53:36 CDT)
- AMBER: bellymask for DNA backbone doesn't seem to work Seth Lilavivat (Thu Jul 03 2008 - 15:13:40 CDT)
- AMBER: about QMMM output linfu (Thu Jul 03 2008 - 21:40:33 CDT)
- AMBER: RESP calculation on Copper containing molecule Vidana.Epa_at_csiro.au (Fri Jul 04 2008 - 02:16:24 CDT)
- AMBER: Boutheina Kerkeni (Fri Jul 04 2008 - 05:34:55 CDT)
- AMBER: trouble interpreting <P2> time correlation function data Sally Pias (Sun Jul 06 2008 - 01:59:57 CDT)
- AMBER: For help: how to perform double decoupling thermodynamic integration calculation in AMBER10 yongleli (Mon Jul 07 2008 - 17:04:53 CDT)
- AMBER: Constant pH with new parameters (amber10) Markus Kaukonen (Tue Jul 08 2008 - 02:39:57 CDT)
- AMBER: [amber/glycam] dealing with fucose... Waqas Nasir (Tue Jul 08 2008 - 09:56:31 CDT)
- AMBER: Force fields for REMD with GB solvent guardiani_at_fi.infn.it (Tue Jul 08 2008 - 11:24:27 CDT)
- AMBER: analysing normal modes Vahdati N. (Tue Jul 08 2008 - 13:03:39 CDT)
- AMBER: Distance diagnolization matrix plot Siddharth Rastogi (Wed Jul 09 2008 - 02:04:08 CDT)
- AMBER: REMD temperature profile guardiani_at_fi.infn.it (Wed Jul 09 2008 - 08:47:13 CDT)
- AMBER: XLeap Problems Schwehm, Jeffrey M. (Wed Jul 09 2008 - 11:26:14 CDT)
- AMBER: amber9 / difference of igb=0 and igb=6 Arturas Ziemys (Wed Jul 09 2008 - 14:45:32 CDT)
- AMBER: Question about loading frcmod.ionsjc_tip3p in xleap Jeff Schwinefus (Wed Jul 09 2008 - 16:27:46 CDT)
- AMBER: ptraj selection Ilyas Yildirim (Wed Jul 09 2008 - 20:07:39 CDT)
- AMBER: mm_pbsa incorrect complex prmtop file xiaonan zhang (Thu Jul 10 2008 - 02:44:58 CDT)
- AMBER: replicas trapped in a few low temperatures Ye Mei (Thu Jul 10 2008 - 04:13:25 CDT)
- AMBER: antechamber and charmm Alan (Thu Jul 10 2008 - 04:43:58 CDT)
- AMBER: bond command Boutheina Kerkeni (Thu Jul 10 2008 - 12:30:46 CDT)
- AMBER: problem with restraints Barbault Florent (Thu Jul 10 2008 - 13:59:15 CDT)
- AMBER: difference between sander and NAB Hu, Shaowen (JSC-SK)[USRA] (Thu Jul 10 2008 - 14:44:41 CDT)
- AMBER: problem with rdparm Harry (Yicun) Ni (Thu Jul 10 2008 - 17:05:41 CDT)
- AMBER: timing info output from pmemd Vlad Cojocaru (Fri Jul 11 2008 - 03:49:28 CDT)
- AMBER: configure_amber (10) for pg compilers Vlad Cojocaru (Fri Jul 11 2008 - 06:51:47 CDT)
- AMBER: size of pdb Boutheina Kerkeni (Fri Jul 11 2008 - 10:13:57 CDT)
- AMBER: question about the improper torsion Harry (Yicun) Ni (Fri Jul 11 2008 - 11:34:17 CDT)
- AMBER: NMA Steve Seibold (Fri Jul 11 2008 - 11:34:00 CDT)
- AMBER: Installation on Mac OSX G5 dual processor George Tzotzos (Fri Jul 11 2008 - 15:30:21 CDT)
- AMBER: Installation of Amber 10 on Dual-Core Intel Mac George Tzotzos (Fri Jul 11 2008 - 15:33:55 CDT)
- AMBER: empty output Boutheina Kerkeni (Sat Jul 12 2008 - 10:29:47 CDT)
- AMBER: Atom type with 10-12 and 6-12 interactions in Amber9 Brad Lambeth (Sat Jul 12 2008 - 19:20:09 CDT)
- AMBER: Nmode entropy calcs Sergio Wong (Sat Jul 12 2008 - 20:09:51 CDT)
- AMBER: Model of deoxyadenosine in Cornell 95 paper Ilyas Yildirim (Sun Jul 13 2008 - 18:14:48 CDT)
- AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Grange Hermitage (Sun Jul 13 2008 - 20:06:33 CDT)
- AMBER: POL3 with gaff and ff02EP Grange Hermitage (Sun Jul 13 2008 - 20:15:43 CDT)
- AMBER: Alanine scanning Khaled Barakat (Sun Jul 13 2008 - 20:50:47 CDT)
- AMBER: querry dipti lele (Mon Jul 14 2008 - 03:05:15 CDT)
- AMBER: Tutorial 6 Beale, John (Mon Jul 14 2008 - 11:48:21 CDT)
- AMBER: bad nonbon in nmode (amber9) Enghui Yap (Mon Jul 14 2008 - 11:25:29 CDT)
- AMBER: Error when performing Alanine scanning Khaled Barakat (Mon Jul 14 2008 - 20:41:26 CDT)
- AMBER: files in Amber directory ( to Junmei Wang ) John Bennett (Tue Jul 15 2008 - 06:10:40 CDT)
- AMBER: ptraj: projection command missing in dispatch.c (AMBER 10) Vlad Cojocaru (Tue Jul 15 2008 - 08:45:11 CDT)
- AMBER: sleap test failures Vlad Cojocaru (Tue Jul 15 2008 - 09:14:23 CDT)
- AMBER: test of parallel sander 10 fail Vlad Cojocaru (Tue Jul 15 2008 - 12:05:51 CDT)
- AMBER: RMSD per residue luzhenw1_at_msu.edu (Tue Jul 15 2008 - 15:28:08 CDT)
- AMBER: Ligand force field generation, and its consistency with the force field of the protein. SeungPyo Hong (Wed Jul 16 2008 - 07:15:48 CDT)
- AMBER: about RMSD per residue luzhenw1_at_msu.edu (Wed Jul 16 2008 - 08:48:05 CDT)
- AMBER: free energy Boutheina Kerkeni (Wed Jul 16 2008 - 10:54:39 CDT)
- AMBER: amber 10 and mpich2 (got eof on console error message from mpich2) Vlad Cojocaru (Thu Jul 17 2008 - 08:30:24 CDT)
- AMBER: SCC-DFTB for Zinc atom Jifeng Wang (Thu Jul 17 2008 - 10:33:15 CDT)
- AMBER: paricular atom coordinates? Vijay Singh (Thu Jul 17 2008 - 11:13:30 CDT)
- AMBER: The list-directed or NAMELIST READ statement cannot be completed rebeca (Thu Jul 17 2008 - 11:42:25 CDT)
- AMBER: AmberTools-1.1 port for FreeBSD M. L. Dodson (Thu Jul 17 2008 - 12:59:05 CDT)
- AMBER: the plot of the groove width versus time for RNA Å·ÑôµÂ·½ (Thu Jul 17 2008 - 18:35:31 CDT)
- AMBER: how to generate psf file using the AMBER topology file tinni sona (Fri Jul 18 2008 - 05:41:11 CDT)
- AMBER: Restarting Problem in MD Simulation khuram sb (Fri Jul 18 2008 - 05:37:07 CDT)
- AMBER: Problems with Frozen atoms julliane Yoneda (Fri Jul 18 2008 - 15:06:54 CDT)
- AMBER: a link for Amber ff ported to Charmm Alan (Sat Jul 19 2008 - 04:07:27 CDT)
- AMBER: parmbsc0 Dr. Suzie Byun (Sat Jul 19 2008 - 10:40:05 CDT)
- AMBER: antechamber generated input for gaussian error Grange Hermitage (Sat Jul 19 2008 - 19:53:49 CDT)
- AMBER: Trans proline dipti lele (Sun Jul 20 2008 - 00:53:00 CDT)
- AMBER: Release of version 1.2 of AmberTools David A. Case (Mon Jul 21 2008 - 12:01:29 CDT)
- AMBER: Where is ICO read from the ix array? Brad Lambeth (Mon Jul 21 2008 - 14:49:44 CDT)
- AMBER: Amber tools 1.2 test failure (installation) Myunggi Yi (Mon Jul 21 2008 - 17:17:05 CDT)
- AMBER: Problem with box dimension in AmberTools ptraj Steve Spronk (Tue Jul 22 2008 - 01:35:47 CDT)
- AMBER: amber ff and how it deals with out-plane chiral C Alan (Tue Jul 22 2008 - 02:59:05 CDT)
- AMBER: targeted MD Germain Vallverdu (Tue Jul 22 2008 - 05:08:04 CDT)
- AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj? Hannes Loeffler (Tue Jul 22 2008 - 09:08:36 CDT)
- AMBER: FreeBSD "port" for AmberTools-1.2 M. L. Dodson (Tue Jul 22 2008 - 14:15:48 CDT)
- AMBER: SHIFTS compile error IN SUK JOUNG (Tue Jul 22 2008 - 15:25:43 CDT)
- AMBER: protonated guanine, cytosine parameters Kliman, Michal (Tue Jul 22 2008 - 17:22:19 CDT)
- AMBER: improper dihedral in ff03 united atom forcefield ÇØæ©æ© (Tue Jul 22 2008 - 20:49:28 CDT)
- AMBER: improper dihedrals in 03 united atom force field Q733 (Tue Jul 22 2008 - 21:00:03 CDT)
- Re: AMBER: improper dihedral in ff03 united atom forcefield Bill Ross (Tue Jul 22 2008 - 23:28:07 CDT)
- AMBER: 1.5ns rst file to PDB file Conversion Error khuram sb (Wed Jul 23 2008 - 00:07:24 CDT)
- AMBER: High force constant for MD ??? Waqas Nasir (Wed Jul 23 2008 - 04:49:46 CDT)
- AMBER: Trans proline dipti lele (Wed Jul 23 2008 - 06:01:28 CDT)
- AMBER: Polarizable force field for divalent ions? Yi-Ming Cheng (Wed Jul 23 2008 - 05:59:08 CDT)
- AMBER: Problems in restrained minimization julliane Yoneda (Wed Jul 23 2008 - 08:08:32 CDT)
- AMBER: Hydroxyproline in AMBER Michael Entz (Wed Jul 23 2008 - 10:40:05 CDT)
- AMBER: Query about the charge of atoms in the parmtop file tinni sona (Wed Jul 23 2008 - 11:48:19 CDT)
- AMBER: Which CO2 potential? Jones de Andrade (Wed Jul 23 2008 - 19:27:58 CDT)
- AMBER: amber9 install problem hklwatergod (Thu Jul 24 2008 - 01:11:33 CDT)
- AMBER: EVB tests failure Vlad Cojocaru (Thu Jul 24 2008 - 03:34:52 CDT)
- AMBER: solvate dna in TIP3PBOX 10.0 Collins Nganou (Thu Jul 24 2008 - 04:28:44 CDT)
- AMBER: adding missing residues soumick (Thu Jul 24 2008 - 06:09:16 CDT)
- AMBER: calculating the enthalpy of evaporation jessica stolee (Thu Jul 24 2008 - 14:24:40 CDT)
- AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 Mike Hanby (Thu Jul 24 2008 - 16:47:34 CDT)
- AMBER: big molecule numbers Adrien Delmont (Thu Jul 24 2008 - 17:27:22 CDT)
- AMBER: solvate dna in TIP3PBOX 10.0 Collins Nganou (Fri Jul 25 2008 - 01:51:54 CDT)
- AMBER: Regarding ff03 forcefield Reena ..... (Fri Jul 25 2008 - 02:24:41 CDT)
- AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Sandeep Kaushik (Fri Jul 25 2008 - 05:04:11 CDT)
- AMBER: amber 10: sander and pmemd performance Vlad Cojocaru (Fri Jul 25 2008 - 04:57:45 CDT)
- AMBER: simulation with many formamide molecules Adrien Delmont (Fri Jul 25 2008 - 05:44:23 CDT)
- AMBER: # of ligands and receptors in mmpbsa Christopher Gaughan (Fri Jul 25 2008 - 09:57:03 CDT)
- AMBER: Energy analysis aneesh cna (Fri Jul 25 2008 - 10:12:10 CDT)
- AMBER: amber10: pmemd gfortran James W. Caldwell (Fri Jul 25 2008 - 13:23:06 CDT)
- AMBER: Does clustering involve fitting? Steve Spronk (Fri Jul 25 2008 - 15:02:09 CDT)
- Re: AMBER: solvate dna in TIP3PBOX 10.0 Bill Ross (Fri Jul 25 2008 - 15:28:46 CDT)
- Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Bill Ross (Fri Jul 25 2008 - 15:40:27 CDT)
- AMBER: fortran runtime error in "make test.serial" with gfortran Jaber Jahanbin Sardroodi (Fri Jul 25 2008 - 17:23:25 CDT)
- AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? Alan (Sat Jul 26 2008 - 03:33:46 CDT)
- AMBER: big molecule numbers ( simulation with many formamide molecules ) Adrien Delmont (Sat Jul 26 2008 - 04:04:08 CDT)
- AMBER: solvate dna in TIP3PBOX 10.0 Collins Nganou (Sat Jul 26 2008 - 04:08:26 CDT)
- AMBER: RE: AMBER Question Ross Walker (Sat Jul 26 2008 - 08:53:25 CDT)
- AMBER: interaction energies in Amber and VMD/NAMD Alessandro Nascimento (Sat Jul 26 2008 - 11:09:38 CDT)
- AMBER: Query dipti lele (Sun Jul 27 2008 - 01:40:54 CDT)
- AMBER: radius of calcium ion in MM_PBSA Hannes Wallnoefer (Mon Jul 28 2008 - 03:18:22 CDT)
- AMBER: Problem in .parmtop file sudipta sinha (Mon Jul 28 2008 - 10:30:09 CDT)
- AMBER: Amber 10 on the BlueGene Mike Hanby (Mon Jul 28 2008 - 11:15:58 CDT)
- Re: AMBER: interaction energies in Amber Alessandro Nascimento (Mon Jul 28 2008 - 19:51:01 CDT)
- AMBER: Energy minimization of protein-ligand complex Dong Xu (Tue Jul 29 2008 - 02:18:57 CDT)
- AMBER: PMEND 9 compilation problems Nick Holway (Tue Jul 29 2008 - 11:04:36 CDT)
- AMBER: for mask in rms Wenyong Tong (Tue Jul 29 2008 - 22:35:23 CDT)
- AMBER: Volume of ucell too big baohua zhang (Tue Jul 29 2008 - 22:30:43 CDT)
- AMBER: DMSOBOX jacopo.sgrignani_at_unifi.it (Wed Jul 30 2008 - 02:05:00 CDT)
- Re: AMBER: interaction energies in Amber and VMD/NAMD (SOLVED) Alessandro Nascimento (Wed Jul 30 2008 - 10:29:47 CDT)
- AMBER: mask for oligosaccharide Wenyong Tong (Wed Jul 30 2008 - 13:23:58 CDT)
- AMBER: Q: ntc = 3 parallel runnable not compiled in Amber 9? Qicun Shi (Wed Jul 30 2008 - 22:51:17 CDT)
- AMBER: how to get the potential energy of a protein from the system TaoPaul (Thu Jul 31 2008 - 03:29:08 CDT)
- AMBER: opls/aa in Amber status Alan (Thu Jul 31 2008 - 03:41:58 CDT)
- AMBER: amb2gmx for big systems rebeca_at_mmb.pcb.ub.es (Thu Jul 31 2008 - 05:40:39 CDT)
- AMBER: ACPYPI announcement Alan (Thu Jul 31 2008 - 06:17:02 CDT)
- AMBER: imin = 5 and PBC sai kumar ramadugu (Thu Jul 31 2008 - 09:51:21 CDT)
- AMBER: prepare an initial structure in Amber oguz gurbulak (Thu Jul 31 2008 - 11:58:24 CDT)
Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:48 CST
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