Amber Archive Jul 2008 by thread
- AMBER: concerning force fields ( to Karl Kirschner ) Adrien Delmont (Tue Jul 01 2008 - 01:04:45 PDT)
- AMBER: Anna Reymer (Tue Jul 01 2008 - 01:36:12 PDT)
- AMBER: AMBER10: ambpdb problems Anna Reymer (Tue Jul 01 2008 - 01:37:38 PDT)
- AMBER: RDF in ptraj fatima.chami.durham.ac.uk (Tue Jul 01 2008 - 06:34:35 PDT)
- AMBER: "radius = 0.000" Arturas Ziemys (Tue Jul 01 2008 - 09:08:45 PDT)
- AMBER: Protonated Phosphate Problem Kliman, Michal (Tue Jul 01 2008 - 10:20:14 PDT)
- Re: AMBER: Regarding force field ff02 and ion library Abhishek Singh (Tue Jul 01 2008 - 12:02:28 PDT)
- AMBER: compile amber10 on Mac Junmei Wang (Tue Jul 01 2008 - 14:45:31 PDT)
- AMBER: parameters for Fe coordinated to four CYS ? Jose Borreguero (Tue Jul 01 2008 - 17:12:37 PDT)
- AMBER: NMR refinement teresa.ierano.unina.it (Wed Jul 02 2008 - 01:38:57 PDT)
- AMBER: NONBONDED_PARM_INDEX Max (Wed Jul 02 2008 - 01:54:35 PDT)
- AMBER: ptraj problem with centering in the box Hannes Wallnoefer (Wed Jul 02 2008 - 07:00:33 PDT)
- AMBER: ptraj problem with imaging fatima.chami.durham.ac.uk (Wed Jul 02 2008 - 09:52:32 PDT)
- AMBER: For help: Thermodynamic Integration of solvation free energy using soft-core potential yongleli (Wed Jul 02 2008 - 11:19:03 PDT)
- AMBER: RED III execution problem ben rodriguez (Wed Jul 02 2008 - 18:24:19 PDT)
- AMBER: How to obtain the oriented trajectories? Panwang Zhou (Thu Jul 03 2008 - 07:06:58 PDT)
- AMBER: PMEMD and polarized force field ff 02 Abhishek Singh (Thu Jul 03 2008 - 07:50:00 PDT)
- AMBER: PMEMD and polarized force field ff 02 Abhishek Singh (Thu Jul 03 2008 - 07:53:36 PDT)
- AMBER: bellymask for DNA backbone doesn't seem to work Seth Lilavivat (Thu Jul 03 2008 - 13:13:40 PDT)
- AMBER: about QMMM output linfu (Thu Jul 03 2008 - 19:40:33 PDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Thu Jul 03 2008 - 23:28:44 PDT)
- AMBER: RESP calculation on Copper containing molecule Vidana.Epa.csiro.au (Fri Jul 04 2008 - 00:16:24 PDT)
- AMBER: Boutheina Kerkeni (Fri Jul 04 2008 - 03:34:55 PDT)
- AMBER: trouble interpreting <P2> time correlation function data Sally Pias (Sat Jul 05 2008 - 23:59:57 PDT)
- AMBER: For help: how to perform double decoupling thermodynamic integration calculation in AMBER10 yongleli (Mon Jul 07 2008 - 15:04:53 PDT)
- AMBER: Constant pH with new parameters (amber10) Markus Kaukonen (Tue Jul 08 2008 - 00:39:57 PDT)
- AMBER: [amber/glycam] dealing with fucose... Waqas Nasir (Tue Jul 08 2008 - 07:56:31 PDT)
- AMBER: Force fields for REMD with GB solvent guardiani.fi.infn.it (Tue Jul 08 2008 - 09:24:27 PDT)
- AMBER: analysing normal modes Vahdati N. (Tue Jul 08 2008 - 11:03:39 PDT)
- AMBER: Distance diagnolization matrix plot Siddharth Rastogi (Wed Jul 09 2008 - 00:04:08 PDT)
- AMBER: REMD temperature profile guardiani.fi.infn.it (Wed Jul 09 2008 - 06:47:13 PDT)
- AMBER: XLeap Problems Schwehm, Jeffrey M. (Wed Jul 09 2008 - 09:26:14 PDT)
- AMBER: amber9 / difference of igb=0 and igb=6 Arturas Ziemys (Wed Jul 09 2008 - 12:45:32 PDT)
- AMBER: analysing normal modes Chris Moth (Wed Jul 09 2008 - 12:45:57 PDT)
- AMBER: Question about loading frcmod.ionsjc_tip3p in xleap Jeff Schwinefus (Wed Jul 09 2008 - 14:27:46 PDT)
- AMBER: ptraj selection Ilyas Yildirim (Wed Jul 09 2008 - 18:07:39 PDT)
- AMBER: mm_pbsa incorrect complex prmtop file xiaonan zhang (Thu Jul 10 2008 - 00:44:58 PDT)
- AMBER: replicas trapped in a few low temperatures Ye Mei (Thu Jul 10 2008 - 02:13:25 PDT)
- AMBER: antechamber and charmm Alan (Thu Jul 10 2008 - 02:43:58 PDT)
- Re: AMBER: pmemd 10 output Vlad Cojocaru (Thu Jul 10 2008 - 03:19:08 PDT)
- AMBER: bond command Boutheina Kerkeni (Thu Jul 10 2008 - 10:30:46 PDT)
- AMBER: problem with restraints Barbault Florent (Thu Jul 10 2008 - 11:59:15 PDT)
- AMBER: difference between sander and NAB Hu, Shaowen (JSC-SK)[USRA] (Thu Jul 10 2008 - 12:44:41 PDT)
- AMBER: problem with rdparm Harry (Yicun) Ni (Thu Jul 10 2008 - 15:05:41 PDT)
- AMBER: timing info output from pmemd Vlad Cojocaru (Fri Jul 11 2008 - 01:49:28 PDT)
- AMBER: configure_amber (10) for pg compilers Vlad Cojocaru (Fri Jul 11 2008 - 04:51:47 PDT)
- AMBER: size of pdb Boutheina Kerkeni (Fri Jul 11 2008 - 08:13:57 PDT)
- AMBER: question about the improper torsion Harry (Yicun) Ni (Fri Jul 11 2008 - 09:34:17 PDT)
- AMBER: NMA Steve Seibold (Fri Jul 11 2008 - 09:34:00 PDT)
- AMBER: Installation on Mac OSX G5 dual processor George Tzotzos (Fri Jul 11 2008 - 13:30:21 PDT)
- AMBER: Installation of Amber 10 on Dual-Core Intel Mac George Tzotzos (Fri Jul 11 2008 - 13:33:55 PDT)
- AMBER: empty output Boutheina Kerkeni (Sat Jul 12 2008 - 08:29:47 PDT)
- AMBER: Atom type with 10-12 and 6-12 interactions in Amber9 Brad Lambeth (Sat Jul 12 2008 - 17:20:09 PDT)
- AMBER: Nmode entropy calcs Sergio Wong (Sat Jul 12 2008 - 18:09:51 PDT)
- AMBER: Model of deoxyadenosine in Cornell 95 paper Ilyas Yildirim (Sun Jul 13 2008 - 16:14:48 PDT)
- AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Grange Hermitage (Sun Jul 13 2008 - 18:06:33 PDT)
- AMBER: POL3 with gaff and ff02EP Grange Hermitage (Sun Jul 13 2008 - 18:15:43 PDT)
- AMBER: Alanine scanning Khaled Barakat (Sun Jul 13 2008 - 18:50:47 PDT)
- AMBER: querry dipti lele (Mon Jul 14 2008 - 01:05:15 PDT)
- AMBER: Tutorial 6 Beale, John (Mon Jul 14 2008 - 09:48:21 PDT)
- AMBER: bad nonbon in nmode (amber9) Enghui Yap (Mon Jul 14 2008 - 09:25:29 PDT)
- AMBER: Error when performing Alanine scanning Khaled Barakat (Mon Jul 14 2008 - 18:41:26 PDT)
- AMBER: files in Amber directory ( to Junmei Wang ) John Bennett (Tue Jul 15 2008 - 04:10:40 PDT)
- AMBER: ptraj: projection command missing in dispatch.c (AMBER 10) Vlad Cojocaru (Tue Jul 15 2008 - 06:45:11 PDT)
- AMBER: sleap test failures Vlad Cojocaru (Tue Jul 15 2008 - 07:14:23 PDT)
- AMBER: test of parallel sander 10 fail Vlad Cojocaru (Tue Jul 15 2008 - 10:05:51 PDT)
- AMBER: RMSD per residue luzhenw1.msu.edu (Tue Jul 15 2008 - 13:28:08 PDT)
- AMBER: Ligand force field generation, and its consistency with the force field of the protein. SeungPyo Hong (Wed Jul 16 2008 - 05:15:48 PDT)
- AMBER: about RMSD per residue luzhenw1.msu.edu (Wed Jul 16 2008 - 06:48:05 PDT)
- AMBER: free energy Boutheina Kerkeni (Wed Jul 16 2008 - 08:54:39 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: SCC-DFTB for Zinc atom Jifeng Wang (Thu Jul 17 2008 - 08:33:15 PDT)
- AMBER: paricular atom coordinates? Vijay Singh (Thu Jul 17 2008 - 09:13:30 PDT)
- AMBER: The list-directed or NAMELIST READ statement cannot be completed rebeca (Thu Jul 17 2008 - 09:42:25 PDT)
- AMBER: AmberTools-1.1 port for FreeBSD M. L. Dodson (Thu Jul 17 2008 - 10:59:05 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: how to generate psf file using the AMBER topology file tinni sona (Fri Jul 18 2008 - 03:41:11 PDT)
- AMBER: Restarting Problem in MD Simulation khuram sb (Fri Jul 18 2008 - 03:37:07 PDT)
- AMBER: Problems with Frozen atoms julliane Yoneda (Fri Jul 18 2008 - 13:06:54 PDT)
- AMBER: a link for Amber ff ported to Charmm Alan (Sat Jul 19 2008 - 02:07:27 PDT)
- AMBER: parmbsc0 Dr. Suzie Byun (Sat Jul 19 2008 - 08:40:05 PDT)
- AMBER: antechamber generated input for gaussian error Grange Hermitage (Sat Jul 19 2008 - 17:53:49 PDT)
- AMBER: Trans proline dipti lele (Sat Jul 19 2008 - 22:53:00 PDT)
- AMBER: Release of version 1.2 of AmberTools David A. Case (Mon Jul 21 2008 - 10:01:29 PDT)
- AMBER: Where is ICO read from the ix array? Brad Lambeth (Mon Jul 21 2008 - 12:49:44 PDT)
- AMBER: Amber tools 1.2 test failure (installation) Myunggi Yi (Mon Jul 21 2008 - 15:17:05 PDT)
- AMBER: Problem with box dimension in AmberTools ptraj Steve Spronk (Mon Jul 21 2008 - 23:35:47 PDT)
- AMBER: amber ff and how it deals with out-plane chiral C Alan (Tue Jul 22 2008 - 00:59:05 PDT)
- AMBER: targeted MD Germain Vallverdu (Tue Jul 22 2008 - 03:08:04 PDT)
- AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj? Hannes Loeffler (Tue Jul 22 2008 - 07:08:36 PDT)
- AMBER: FreeBSD "port" for AmberTools-1.2 M. L. Dodson (Tue Jul 22 2008 - 12:15:48 PDT)
- AMBER: SHIFTS compile error IN SUK JOUNG (Tue Jul 22 2008 - 13:25:43 PDT)
- AMBER: protonated guanine, cytosine parameters Kliman, Michal (Tue Jul 22 2008 - 15:22:19 PDT)
- AMBER: improper dihedral in ff03 united atom forcefield 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)
- Re: AMBER: improper dihedral in ff03 united atom forcefield Bill Ross (Tue Jul 22 2008 - 21:28:07 PDT)
- AMBER: 1.5ns rst file to PDB file Conversion Error khuram sb (Tue Jul 22 2008 - 22:07:24 PDT)
- AMBER: High force constant for MD ??? Waqas Nasir (Wed Jul 23 2008 - 02:49:46 PDT)
- AMBER: Polarizable force field for divalent ions? Yi-Ming Cheng (Wed Jul 23 2008 - 03:59:08 PDT)
- AMBER: Trans proline dipti lele (Wed Jul 23 2008 - 04:01:28 PDT)
- AMBER: Problems in restrained minimization julliane Yoneda (Wed Jul 23 2008 - 06:08:32 PDT)
- AMBER: Hydroxyproline in AMBER Michael Entz (Wed Jul 23 2008 - 08:40:05 PDT)
- AMBER: Query about the charge of atoms in the parmtop file tinni sona (Wed Jul 23 2008 - 09:48:19 PDT)
- AMBER: Which CO2 potential? Jones de Andrade (Wed Jul 23 2008 - 17:27:58 PDT)
- AMBER: amber9 install problem hklwatergod (Wed Jul 23 2008 - 23:11:33 PDT)
- AMBER: EVB tests failure Vlad Cojocaru (Thu Jul 24 2008 - 01:34:52 PDT)
- AMBER: solvate dna in TIP3PBOX 10.0 Collins Nganou (Thu Jul 24 2008 - 02:28:44 PDT)
- AMBER: adding missing residues soumick (Thu Jul 24 2008 - 04:09:16 PDT)
- AMBER: calculating the enthalpy of evaporation jessica stolee (Thu Jul 24 2008 - 12:24:40 PDT)
- AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 Mike Hanby (Thu Jul 24 2008 - 14:47:34 PDT)
- AMBER: big molecule numbers Adrien Delmont (Thu Jul 24 2008 - 15:27:22 PDT)
- AMBER: solvate dna in TIP3PBOX 10.0 Collins Nganou (Thu Jul 24 2008 - 23:51:54 PDT)
- AMBER: Regarding ff03 forcefield Reena ..... (Fri Jul 25 2008 - 00:24:41 PDT)
- AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Sandeep Kaushik (Fri Jul 25 2008 - 03:04:11 PDT)
- AMBER: amber 10: sander and pmemd performance Vlad Cojocaru (Fri Jul 25 2008 - 02:57:45 PDT)
- AMBER: simulation with many formamide molecules Adrien Delmont (Fri Jul 25 2008 - 03:44:23 PDT)
- AMBER: # of ligands and receptors in mmpbsa Christopher Gaughan (Fri Jul 25 2008 - 07:57:03 PDT)
- AMBER: Energy analysis aneesh cna (Fri Jul 25 2008 - 08:12:10 PDT)
- AMBER: amber10: pmemd gfortran James W. Caldwell (Fri Jul 25 2008 - 11:23:06 PDT)
- AMBER: Does clustering involve fitting? Steve Spronk (Fri Jul 25 2008 - 13:02:09 PDT)
- Re: AMBER: solvate dna in TIP3PBOX 10.0 Bill Ross (Fri Jul 25 2008 - 13:28:46 PDT)
- Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Bill Ross (Fri Jul 25 2008 - 13:40:27 PDT)
- AMBER: fortran runtime error in "make test.serial" with gfortran Jaber Jahanbin Sardroodi (Fri Jul 25 2008 - 15:23:25 PDT)
- AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? Alan (Sat Jul 26 2008 - 01:33:46 PDT)
- AMBER: big molecule numbers ( simulation with many formamide molecules ) Adrien Delmont (Sat Jul 26 2008 - 02:04:08 PDT)
- AMBER: solvate dna in TIP3PBOX 10.0 Collins Nganou (Sat Jul 26 2008 - 02:08:26 PDT)
- AMBER: RE: AMBER Question Ross Walker (Sat Jul 26 2008 - 06:53:25 PDT)
- AMBER: interaction energies in Amber and VMD/NAMD Alessandro Nascimento (Sat Jul 26 2008 - 09:09:38 PDT)
- AMBER: the install problem hklwatergod (Sat Jul 26 2008 - 23:34:55 PDT)
- AMBER: Query dipti lele (Sat Jul 26 2008 - 23:40:54 PDT)
- AMBER: radius of calcium ion in MM_PBSA Hannes Wallnoefer (Mon Jul 28 2008 - 01:18:22 PDT)
- AMBER: Problem in .parmtop file sudipta sinha (Mon Jul 28 2008 - 08:30:09 PDT)
- AMBER: Amber 10 on the BlueGene Mike Hanby (Mon Jul 28 2008 - 09:15:58 PDT)
- Re: AMBER: interaction energies in Amber Alessandro Nascimento (Mon Jul 28 2008 - 17:51:01 PDT)
- AMBER: Energy minimization of protein-ligand complex Dong Xu (Tue Jul 29 2008 - 00:18:57 PDT)
- AMBER: PMEND 9 compilation problems Nick Holway (Tue Jul 29 2008 - 09:04:36 PDT)
- AMBER: Volume of ucell too big baohua zhang (Tue Jul 29 2008 - 20:30:43 PDT)
- AMBER: for mask in rms Wenyong Tong (Tue Jul 29 2008 - 20:35:23 PDT)
- AMBER: DMSOBOX jacopo.sgrignani.unifi.it (Wed Jul 30 2008 - 00:05:00 PDT)
- Re: AMBER: Prepgen Heikki Salo (Wed Jul 30 2008 - 01:58:28 PDT)
- Re: AMBER: interaction energies in Amber and VMD/NAMD (SOLVED) Alessandro Nascimento (Wed Jul 30 2008 - 08:29:47 PDT)
- AMBER: mask for oligosaccharide Wenyong Tong (Wed Jul 30 2008 - 11:23:58 PDT)
- AMBER: Q: ntc = 3 parallel runnable not compiled in Amber 9? Qicun Shi (Wed Jul 30 2008 - 20:51:17 PDT)
- AMBER: how to get the potential energy of a protein from the system TaoPaul (Thu Jul 31 2008 - 01:29:08 PDT)
- AMBER: opls/aa in Amber status Alan (Thu Jul 31 2008 - 01:41:58 PDT)
- AMBER: amb2gmx for big systems rebeca.mmb.pcb.ub.es (Thu Jul 31 2008 - 03:40:39 PDT)
- AMBER: ACPYPI announcement Alan (Thu Jul 31 2008 - 04:17:02 PDT)
- AMBER: imin = 5 and PBC sai kumar ramadugu (Thu Jul 31 2008 - 07:51:21 PDT)
- AMBER: prepare an initial structure in Amber oguz gurbulak (Thu Jul 31 2008 - 09:58:24 PDT)
- Last message date: Sun Aug 03 2008 - 06:07:39 PDT
- Archived on: Fri Nov 22 2024 - 05:53:40 PST
