Amber Archive Jun 2007 by thread
- Re: AMBER: Solvent models Francesco Pietra (Fri Jun 01 2007 - 00:00:36 PDT)
- AMBER: problem in installing amber9 Syed Tarique Moin (Fri Jun 01 2007 - 00:10:44 PDT)
- AMBER: rms in nmode Marie Brut (Fri Jun 01 2007 - 00:22:22 PDT)
- AMBER: Question about separating bonded force Shawn yy (Fri Jun 01 2007 - 08:31:04 PDT)
- AMBER: equilibrium constants via MMPBSA Sean Rathlef (Fri Jun 01 2007 - 09:57:46 PDT)
- Re: AMBER: Reg restraint value obtained during umbrella sampling D.Usharani (Fri Jun 01 2007 - 10:12:23 PDT)
- AMBER: BUG? Does TLEAP understand SPC/E water? David Cerutti (Fri Jun 01 2007 - 10:35:02 PDT)
- AMBER: RE: process_mdout.perl Ross Walker (Fri Jun 01 2007 - 12:47:04 PDT)
- AMBER: "distance" command in ptraj Roberto Veiga (Sat Jun 02 2007 - 04:19:42 PDT)
- AMBER: pdb flie format Mr Defang Ouyang (Sun Jun 03 2007 - 05:53:08 PDT)
- AMBER: dihedral simulation lishan yao (Sun Jun 03 2007 - 08:49:33 PDT)
- AMBER: MM-GBSA: pairwise decompose energy calculation can't read snapshot_com.all.out jitrayut jitonnom (Sun Jun 03 2007 - 09:08:16 PDT)
- Re: AMBER: RESTRAINTMASK Sandeep Kaushik (Sun Jun 03 2007 - 22:38:21 PDT)
- AMBER: LES problem Urszula Uciechowska (Mon Jun 04 2007 - 06:34:42 PDT)
- AMBER: Once again, "distance" command in ptraj Roberto Veiga (Mon Jun 04 2007 - 07:06:19 PDT)
- AMBER: Once again, "distance" command in ptraj Roberto Veiga (Mon Jun 04 2007 - 09:47:01 PDT)
- AMBER: Amber9's sander.MPI on x86_64 kkirschn.hamilton.edu (Mon Jun 04 2007 - 10:13:51 PDT)
- AMBER: Problem about prepare the model when running antechamber Liang, Lei (Mon Jun 04 2007 - 13:04:36 PDT)
- AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... Sophie Barbe (Mon Jun 04 2007 - 14:16:48 PDT)
- AMBER: problem with starting REM on amber9 priya priya (Tue Jun 05 2007 - 06:32:50 PDT)
- AMBER: Ptraj hbond analysis Achuth Prabhu (Tue Jun 05 2007 - 07:51:54 PDT)
- AMBER: problem running parallel jobs Nikola Trbovic (Tue Jun 05 2007 - 13:43:02 PDT)
- AMBER: REMD and mpiexec Steve Young (Tue Jun 05 2007 - 17:53:14 PDT)
- AMBER: g(r) in mixtures? BJÖRN KARLSSON (Wed Jun 06 2007 - 00:56:05 PDT)
- AMBER: Restraining valence angles Abi Ghanem josephine (Wed Jun 06 2007 - 01:35:12 PDT)
- AMBER: Reg COM restraint to DNA D.Usharani (Wed Jun 06 2007 - 02:56:00 PDT)
- AMBER: GB vs. Invacuo Energies Seth Lilavivat (Wed Jun 06 2007 - 07:38:32 PDT)
- AMBER: Hardware recommendations please Jeremy Weedon (Wed Jun 06 2007 - 09:15:16 PDT)
- AMBER: Ptraj: reading PDB files Austin B. Yongye (Wed Jun 06 2007 - 14:37:31 PDT)
- AMBER: How to fix two angle but do umberlla sampling for distance? Catein Catherine (Thu Jun 07 2007 - 08:14:30 PDT)
- AMBER: Should we just vary one parameter at a time only for PMF calculations? Catein Catherine (Thu Jun 07 2007 - 08:18:51 PDT)
- AMBER: extracting starting structures from equilibration trajectory Nikola Trbovic (Thu Jun 07 2007 - 11:06:15 PDT)
- AMBER: Dihedral driver Beale, John (Thu Jun 07 2007 - 13:08:35 PDT)
- AMBER: amber94 parameters for cholesterol paula lario (Thu Jun 07 2007 - 15:57:38 PDT)
- AMBER: Trouble on wiki about GAFF j j (Thu Jun 07 2007 - 16:29:37 PDT)
- AMBER: mmpbsa decomposition error cristian (Fri Jun 08 2007 - 08:34:21 PDT)
- AMBER: Compiling openmpi/icc/icpc Francesco Pietra (Fri Jun 08 2007 - 10:27:20 PDT)
- AMBER: Taryn Hartley (Fri Jun 08 2007 - 11:39:15 PDT)
- AMBER: RE: Need your gudiance Ross Walker (Fri Jun 08 2007 - 14:18:23 PDT)
- AMBER: RE: Need your gudiance Ross Walker (Fri Jun 08 2007 - 14:24:47 PDT)
- AMBER: antechamber/charges/conformation Francesco Pietra (Sun Jun 10 2007 - 00:02:15 PDT)
- AMBER: amber9 compile problem hmeij.wesleyan.edu (Sun Jun 10 2007 - 06:58:54 PDT)
- AMBER: problem installing amber7 Saiful Islam (Sun Jun 10 2007 - 07:55:19 PDT)
- AMBER: Rdf question BJÖRN KARLSSON (Sun Jun 10 2007 - 12:51:16 PDT)
- AMBER: Installing on windows Colby C (Sun Jun 10 2007 - 16:42:25 PDT)
- AMBER: Steve Seibold (Mon Jun 11 2007 - 10:31:47 PDT)
- AMBER: Question about MPI-IO David LeBard (Mon Jun 11 2007 - 13:58:54 PDT)
- AMBER: dihedral parameters Jardas sucuriba (Mon Jun 11 2007 - 15:13:36 PDT)
- AMBER: Amber 9 on IRIX 6.5 Colby C (Mon Jun 11 2007 - 18:55:25 PDT)
- AMBER: xleap on cygwin Colby C (Mon Jun 11 2007 - 18:59:17 PDT)
- AMBER: NMR vs. X-ray structures Sally Pias (Mon Jun 11 2007 - 22:22:19 PDT)
- AMBER: Amber: Number density profile, pucker..reg Praveena Gopal (Mon Jun 11 2007 - 23:17:37 PDT)
- AMBER: building water box with desired number of molecules Vijay Manickam Achari (Tue Jun 12 2007 - 00:33:21 PDT)
- AMBER: Internal dielectric and MMPBSA Ileana Stoica (Tue Jun 12 2007 - 04:32:17 PDT)
- AMBER: Metal ions in GBSA Wei Chen (Tue Jun 12 2007 - 06:13:36 PDT)
- AMBER: Using position restraints during constant pressure equilibration priya priya (Tue Jun 12 2007 - 06:17:44 PDT)
- AMBER: MM-PBSA calcuation for drug dna complex in 2:1 ratio saurabh agrawal (Tue Jun 12 2007 - 06:25:09 PDT)
- AMBER: Steve Seibold (Tue Jun 12 2007 - 09:21:15 PDT)
- RE: AMBER: Atom types Taryn Hartley (Tue Jun 12 2007 - 10:25:30 PDT)
- AMBER: box size bomb in QMMM calculation M. L. Dodson (Tue Jun 12 2007 - 12:46:00 PDT)
- AMBER: frcmod Brooke Elizabeth Adams (Tue Jun 12 2007 - 13:38:50 PDT)
- AMBER: metal ions Wei Chen (Tue Jun 12 2007 - 14:20:26 PDT)
- AMBER: Installing amber9 in IBM P5? Du, Shiyu (Tue Jun 12 2007 - 19:09:34 PDT)
- AMBER: hydrogen bond Guillaume Renvez (Wed Jun 13 2007 - 01:49:22 PDT)
- AMBER: problems using TIP4PBOX john chen (Wed Jun 13 2007 - 03:53:30 PDT)
- AMBER: [Fwd: Tr: H bonds] Guillaume Renvez (Wed Jun 13 2007 - 05:37:20 PDT)
- AMBER: Hbonds mbrut.laas.fr (Wed Jun 13 2007 - 05:54:52 PDT)
- AMBER: S-nitrocysteine Anthony Cruz Balberdi (Wed Jun 13 2007 - 06:12:00 PDT)
- AMBER: g(r) khn _ (Wed Jun 13 2007 - 09:43:25 PDT)
- AMBER: SANDER error: 'angles are not correct' Fred Baba (Wed Jun 13 2007 - 14:47:14 PDT)
- AMBER: Regarding conversion of CHARMM force field parameters to AMBER parameters. nag raj (Wed Jun 13 2007 - 20:58:22 PDT)
- THANKS -- Re: AMBER: NMR vs. X-ray structures Sally Pias (Wed Jun 13 2007 - 21:33:06 PDT)
- AMBER: (no subject) Catein Catherine (Wed Jun 13 2007 - 22:54:28 PDT)
- AMBER: Hbonds mbrut.laas.fr (Thu Jun 14 2007 - 00:45:25 PDT)
- AMBER: ff99 vs ff99SB for RNA Brent Krueger (Thu Jun 14 2007 - 07:05:12 PDT)
- AMBER: [ProblemSolved]Re: SANDER error: 'angles are not correct' Fred Baba (Thu Jun 14 2007 - 10:08:47 PDT)
- AMBER: Compile openmpi Francesco Pietra (Thu Jun 14 2007 - 10:11:02 PDT)
- AMBER: umbrella sampling dihedral restraint question Cen Gao (Thu Jun 14 2007 - 13:33:51 PDT)
- AMBER: pair distribution function khn _ (Thu Jun 14 2007 - 16:20:47 PDT)
- AMBER: isolated NTP Steve Seibold (Fri Jun 15 2007 - 07:07:16 PDT)
- AMBER: Saving a structuring from trajectory Seth Lilavivat (Fri Jun 15 2007 - 11:42:12 PDT)
- Re: AMBER: Amber Installation Error David A. Case (Fri Jun 15 2007 - 11:56:29 PDT)
- RE: AMBER: Amber Installation Error Ross Walker (Fri Jun 15 2007 - 12:25:28 PDT)
- AMBER: .lib files Taryn Hartley (Fri Jun 15 2007 - 12:42:16 PDT)
- AMBER: performance with implicit solvent Kijeong Kwac (Fri Jun 15 2007 - 13:02:49 PDT)
- AMBER: PDB problems Taryn Hartley (Fri Jun 15 2007 - 13:17:13 PDT)
- Re: AMBER: Saving a structuring from trajectory Bill Ross (Fri Jun 15 2007 - 13:43:23 PDT)
- AMBER: MMPBSA-nmode .top question Matthew Danielson (Fri Jun 15 2007 - 14:11:52 PDT)
- AMBER: Energy outputs in TI Approach Ilyas Yildirim (Fri Jun 15 2007 - 22:03:26 PDT)
- AMBER: distance scan Miguel Ferreira (Sat Jun 16 2007 - 03:16:15 PDT)
- AMBER: distance scan Miguel Ferreira (Sat Jun 16 2007 - 03:25:59 PDT)
- AMBER: implementation of GB model in AMBER john chen (Sun Jun 17 2007 - 05:49:24 PDT)
- AMBER: error due to exceeding left-hand side digital numbers in restart output Cenk Andac (Mon Jun 18 2007 - 01:09:36 PDT)
- AMBER: problem with running rem on amber9 priya priya (Mon Jun 18 2007 - 05:41:02 PDT)
- AMBER: Charge not integral. Head-to-tail cyclic peptides Giacomo Bastianelli (Mon Jun 18 2007 - 06:55:46 PDT)
- Re: AMBER: problem with running rem on amber9 (NOT A REMD PROBLEM) Carlos Simmerling (Mon Jun 18 2007 - 08:31:19 PDT)
- AMBER: shell model MD Stern, Julie (Mon Jun 18 2007 - 09:48:54 PDT)
- AMBER: Questions about how ptraj calculates solvent shells Roberto Veiga (Mon Jun 18 2007 - 11:46:59 PDT)
- AMBER: unres Carra, Claudio (JSC-SK)[USRA] (Mon Jun 18 2007 - 13:55:20 PDT)
- AMBER: H bond Guillaume Renvez (Tue Jun 19 2007 - 01:18:45 PDT)
- AMBER: Re: Strange shape in my MD simulations Pavan G (Tue Jun 19 2007 - 05:47:58 PDT)
- AMBER: How to add semi-experience parameter in divcon? clarkzhy (Tue Jun 19 2007 - 07:23:04 PDT)
- AMBER: Reply regarding PCA with ptraj and IED Steve Spronk (Tue Jun 19 2007 - 14:00:37 PDT)
- AMBER: problems in adding ACE and NME group backy (Wed Jun 20 2007 - 02:09:26 PDT)
- AMBER: Re: Fwd: joshua j j (Wed Jun 20 2007 - 04:27:43 PDT)
- AMBER: 5 Ligands and 1 Protein Colby C (Wed Jun 20 2007 - 11:07:33 PDT)
- AMBER: Algorithm for integration of equations of motion Roberto Veiga (Wed Jun 20 2007 - 11:55:45 PDT)
- AMBER: sander core dumped during minimization zgleo (Wed Jun 20 2007 - 18:51:04 PDT)
- AMBER: set up system solution with 3 different components, each with multiple copies Nicolas Lux Fawzi (Thu Jun 21 2007 - 08:56:57 PDT)
- AMBER: ptray segfault: vector out Nicolas Lux Fawzi (Thu Jun 21 2007 - 12:19:49 PDT)
- To Mr. Ross Walker Re: RE: AMBER: How to add semi-experience parameter in divcon? clarkzhy (Thu Jun 21 2007 - 18:19:23 PDT)
- AMBER: testing protein stability Sally Pias (Thu Jun 21 2007 - 22:24:58 PDT)
- AMBER: Limitation in number of atoms/residues Sascha Rehm (Fri Jun 22 2007 - 03:47:35 PDT)
- AMBER: radius of gyration priya priya (Fri Jun 22 2007 - 08:10:36 PDT)
- AMBER: remd/rdc's McElheny, Dan (Fri Jun 22 2007 - 11:04:59 PDT)
- AMBER: radial distribution function in ptraj khn _ (Fri Jun 22 2007 - 18:25:05 PDT)
- AMBER: SPCFW water: angle problems in leap Thomas Hofer (Sat Jun 23 2007 - 09:02:32 PDT)
- AMBER: Antechamber--Boron Parameters brmeher.iitg.ernet.in (Mon Jun 25 2007 - 03:04:30 PDT)
- AMBER: how to calculate energy of the peptide priya priya (Mon Jun 25 2007 - 06:56:54 PDT)
- AMBER: environment variables Francesco Pietra (Mon Jun 25 2007 - 08:51:05 PDT)
- AMBER: RDF of pure chloroform BJÖRN KARLSSON (Mon Jun 25 2007 - 08:56:19 PDT)
- AMBER: sander MPI fails included tests Sergio Wong (Mon Jun 25 2007 - 10:20:55 PDT)
- AMBER: Re: ff02 and ff03 parameters Pavan G (Mon Jun 25 2007 - 12:34:30 PDT)
- AMBER: PMF calculation Jena M (Mon Jun 25 2007 - 12:59:02 PDT)
- AMBER: Simulated Annealing Joseph Maxwell (Mon Jun 25 2007 - 16:28:14 PDT)
- AMBER: PBSA Error Pankaj R. Daga (Tue Jun 26 2007 - 07:03:41 PDT)
- AMBER: rst overflow for implicit REMD In Hee Park (Tue Jun 26 2007 - 07:37:45 PDT)
- AMBER: $AMBERHOME on PATH Francesco Pietra (Tue Jun 26 2007 - 10:38:35 PDT)
- AMBER: "FATAL: Atom xxx does not have a type." Fred Baba (Tue Jun 26 2007 - 10:59:51 PDT)
- AMBER: Unexpected Failure in XLeap Jason Brown (Tue Jun 26 2007 - 11:45:14 PDT)
- AMBER: Does Chimera support AMBER file formats? Ilyas Yildirim (Tue Jun 26 2007 - 16:58:56 PDT)
- Fwd: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Wed Jun 27 2007 - 07:30:09 PDT)
- Fwd: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Wed Jun 27 2007 - 07:59:02 PDT)
- Fwd: Re: AMBER: $AMBERHOME on PATH & compilations Francesco Pietra (Wed Jun 27 2007 - 09:10:38 PDT)
- AMBER: bugfix.all Francesco Pietra (Wed Jun 27 2007 - 13:26:15 PDT)
- AMBER: how to stop ptraj atom renumbering Russell Green (Wed Jun 27 2007 - 13:25:53 PDT)
- AMBER: Math libraries Francesco Pietra (Thu Jun 28 2007 - 02:56:45 PDT)
- AMBER: conversion of Macromodel substructure format to .frcmod file brmeher.iitg.ernet.in (Thu Jun 28 2007 - 03:24:24 PDT)
- AMBER: Improving pmemd parallel scaling Alessandro Nascimento (Thu Jun 28 2007 - 09:07:15 PDT)
- AMBER: Problem with leaprc yen li (Thu Jun 28 2007 - 20:27:52 PDT)
- Fwd: RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Thu Jun 28 2007 - 22:58:19 PDT)
- AMBER: Sander Error Colby C (Fri Jun 29 2007 - 07:47:05 PDT)
- AMBER: Fwd: Serial "make" failure with xleap Francesco Pietra (Fri Jun 29 2007 - 10:26:54 PDT)
- AMBER: Serial "make" failure Francesco Pietra (Fri Jun 29 2007 - 13:59:42 PDT)
- AMBER: make serial failure for xleap Francesco Pietra (Fri Jun 29 2007 - 14:05:52 PDT)
- Fwd: Re: AMBER: make serial failure for xleap Francesco Pietra (Sat Jun 30 2007 - 06:00:31 PDT)
- AMBER: amber7 and xleap Saiful Islam (Sat Jun 30 2007 - 06:14:21 PDT)
- Fwd: Re: AMBER: make test serial Francesco Pietra (Sat Jun 30 2007 - 06:42:56 PDT)
- AMBER: MM-PBSA POPC/TIP3P/GPCR/LIGAND Jojart Balazs (Sat Jun 30 2007 - 11:25:49 PDT)
- Last message date: Sun Jul 01 2007 - 06:07:55 PDT
- Archived on: Wed Dec 25 2024 - 05:53:38 PST
