Amber Archive Oct 2005 By Thread
- AMBER: Error check COM velocity!! jpragati.ibab.ac.in (Mon Oct 03 2005 - 04:58:01 PDT)
- AMBER: cut-offs in non-periodic simulations Fabien Cailliez (Mon Oct 03 2005 - 09:31:26 PDT)
- Re: AMBER: amber8 parallel sander Kathleen Erickson (Mon Oct 03 2005 - 13:37:47 PDT)
- AMBER: question temperature coupling tautp value for RNA Zhuang (Mon Oct 03 2005 - 15:40:23 PDT)
- AMBER: question temperature coupling tautp value for RNA Zhuang (Mon Oct 03 2005 - 15:40:09 PDT)
- AMBER: Problem during production!! jpragati.ibab.ac.in (Tue Oct 04 2005 - 01:33:48 PDT)
- AMBER: Can I trust ANAL result? Madjid Taghdir (Tue Oct 04 2005 - 03:55:51 PDT)
- AMBER: Manganese ion parameter nadtanet (Tue Oct 04 2005 - 04:55:59 PDT)
- AMBER: Energy output problem! Pradipta Bandyopadhyay (Tue Oct 04 2005 - 05:08:04 PDT)
- AMBER: The default of HIS in leaprc : HID or HIE ? Jiten (Tue Oct 04 2005 - 09:21:52 PDT)
- AMBER: Fw: The default of HIS in leaprc : HID or HIE ? Jiten (Tue Oct 04 2005 - 09:34:54 PDT)
- AMBER: Installation error - icc: command not found Sukjoon Yoon (Tue Oct 04 2005 - 18:13:11 PDT)
- AMBER: Is AMBER package suitable for simulating multiple molecule in solvent? wulei (Wed Oct 05 2005 - 02:26:00 PDT)
- AMBER: antechamber dimesion size, again Toshifumi Yui (Thu Oct 06 2005 - 02:44:29 PDT)
- Re: AMBER: Minimization in sander and nmode David A. Case (Thu Oct 06 2005 - 03:06:33 PDT)
- AMBER: question about grid in ptraj Linchen Gong (Thu Oct 06 2005 - 06:03:00 PDT)
- AMBER: R factors in NMR intensity refinement Yuqin Cai (Thu Oct 06 2005 - 09:29:31 PDT)
- AMBER: AMBER compilation error Sukjoon Yoon (Thu Oct 06 2005 - 19:32:36 PDT)
- AMBER: QMMM question xiaoqin huang (Thu Oct 06 2005 - 21:09:53 PDT)
- AMBER: parameters for pyridoxal phosphate Anna Feldman-Salit (Fri Oct 07 2005 - 06:46:29 PDT)
- AMBER: problem with temperature weights Manish Datt (Fri Oct 07 2005 - 08:43:52 PDT)
- Re: AMBER: How to get PDB structures optimized for RED-II Cenk Andac (Sat Oct 08 2005 - 06:34:42 PDT)
- AMBER: sander error Yam (Sun Oct 09 2005 - 19:04:20 PDT)
- AMBER: Parameters and topology for Diacylglycerol (DAG) Nitin Bhardwaj (Mon Oct 10 2005 - 11:02:14 PDT)
- AMBER: how to constitute T-phosphotyrosine group? luaj.sohu.com (Tue Oct 11 2005 - 05:28:38 PDT)
- AMBER: PCA Claire Zerafa (Tue Oct 11 2005 - 06:33:49 PDT)
- AMBER: how can I constitute T-phosphotyrosine group ? luaj.sohu.com (Tue Oct 11 2005 - 07:25:02 PDT)
- AMBER: maxgrp error Javier Pérez Mirón (Tue Oct 11 2005 - 12:55:46 PDT)
- AMBER: warning in leap Marcela Madrid (Tue Oct 11 2005 - 14:26:42 PDT)
- AMBER: How to simulate a crystal structure? Chunhu Tan (Tue Oct 11 2005 - 16:22:39 PDT)
- AMBER: F,Cl,Br,I in MMPBSA Yong Xu (Wed Oct 12 2005 - 01:58:53 PDT)
- AMBER: troubleshooting replica exchange Zhuang (Wed Oct 12 2005 - 16:46:08 PDT)
- AMBER: how can I constitute T-phosphotyrosine group ? luaj.sohu.com (Wed Oct 12 2005 - 21:50:16 PDT)
- AMBER: AMBER goes in a Loop Imran Khan (Thu Oct 13 2005 - 10:05:40 PDT)
- AMBER: Scaling factor of NMR restraint FyD (Fri Oct 14 2005 - 07:28:24 PDT)
- AMBER: oxidised methionine residue Megan G (Fri Oct 14 2005 - 08:45:21 PDT)
- AMBER: again: F, Cl, Br, I in MMPBSA Yong Xu (Fri Oct 14 2005 - 20:07:59 PDT)
- AMBER: GNU Autotool integration for Amber8! mk mk (Sun Oct 16 2005 - 00:06:11 PDT)
- AMBER: Free energy for L and D amino acids S.Sundar Raman (Sun Oct 16 2005 - 08:40:24 PDT)
- AMBER: Cyclohexane solvent Box chaiann ng (Sun Oct 16 2005 - 21:43:21 PDT)
- AMBER: antechamber -- missing improper torsions David Mobley (Mon Oct 17 2005 - 11:33:43 PDT)
- AMBER: pca with ptraj Claire Zerafa (Mon Oct 17 2005 - 16:11:21 PDT)
- AMBER: program to visualize crystal symmetries Hannes Loeffler (Tue Oct 18 2005 - 01:36:31 PDT)
- AMBER: problem with xleap Vlad Cojocaru (Tue Oct 18 2005 - 06:56:38 PDT)
- AMBER: Simple 3D Molecule Visualization Alec M. Resnick (Tue Oct 18 2005 - 09:29:43 PDT)
- AMBER: Neutral C-terminal residue Sébastien Fiorucci (Wed Oct 19 2005 - 03:12:44 PDT)
- AMBER: Fw: pca with ptraj Claire Zerafa (Wed Oct 19 2005 - 05:02:08 PDT)
- AMBER: ptraj hbond analysis S.Sundar Raman (Wed Oct 19 2005 - 06:28:09 PDT)
- AMBER: amber file formats. Shishir (Wed Oct 19 2005 - 13:16:04 PDT)
- AMBER: (no subject) mathew k varghese (Wed Oct 19 2005 - 22:19:06 PDT)
- AMBER: porblem in ptraj julien (Thu Oct 20 2005 - 02:19:47 PDT)
- AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue haixiao jin (Thu Oct 20 2005 - 03:49:29 PDT)
- AMBER: REMD error!!! Anthony Cruz (Thu Oct 20 2005 - 06:53:18 PDT)
- AMBER: delphi and surface in MMPBSA Yong Xu (Thu Oct 20 2005 - 07:07:17 PDT)
- AMBER: Targeted MD Whitney Allen (Thu Oct 20 2005 - 11:04:31 PDT)
- AMBER: xleap with modified residue Whitney Allen (Thu Oct 20 2005 - 11:12:42 PDT)
- Re: (2) Re: AMBER: F,Cl,Br,I in MMPBSA Yong Xu (Thu Oct 20 2005 - 18:21:33 PDT)
- AMBER: Dipolar coupling refinement s0344557.sms.ed.ac.uk (Fri Oct 21 2005 - 06:04:39 PDT)
- AMBER: using position restraints in target MD? Ben-Zhuo Lu (Fri Oct 21 2005 - 11:58:05 PDT)
- Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA JunJun Liu (Sat Oct 22 2005 - 00:45:25 PDT)
- Problem solved! Re: AMBER: How to get PDB structures optimized for RED-II Cenk Andac (Sat Oct 22 2005 - 10:38:58 PDT)
- Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED Cenk Andac (Sat Oct 22 2005 - 11:02:00 PDT)
- AMBER: Hi..I am new to AMBER.(compilation with MPICH-G2 libraries)... konnipati murali (Sat Oct 22 2005 - 23:38:28 PDT)
- AMBER: rdparm: a parameter array overflowed ying xiong (Mon Oct 24 2005 - 02:17:33 PDT)
- AMBER: compiling amber with pgi 5.2.4 Hannes Barsch (Mon Oct 24 2005 - 05:21:11 PDT)
- AMBER: error in safe Claire Zerafa (Mon Oct 24 2005 - 06:18:50 PDT)
- AMBER: Is MM-PBSA doable for transition metals ? Cenk Andac (Mon Oct 24 2005 - 09:55:27 PDT)
- Re: AMBER: Is MM-PBSA doable for transition metals ? Bill Ross (Mon Oct 24 2005 - 10:10:44 PDT)
- AMBER: atmtypenumbers Yong Xu (Mon Oct 24 2005 - 20:25:00 PDT)
- AMBER: How to calculate binding free energy of ligand bound to complex with two active-site water molecules? haixiao jin (Tue Oct 25 2005 - 00:55:46 PDT)
- AMBER: Using RED to calculate partial charges of new amino acid Donald Thomas (Tue Oct 25 2005 - 07:50:40 PDT)
- AMBER: I am looking forward to hearing from you. Mehdi Davari (Tue Oct 25 2005 - 11:38:28 PDT)
- AMBER: parmchk error : Cannot open CONNECT.TPL, exit Nitin Bhardwaj (Tue Oct 25 2005 - 14:08:02 PDT)
- AMBER: Antechamber error Nitin Bhardwaj (Tue Oct 25 2005 - 16:27:39 PDT)
- AMBER: AMBER tests (x86-64, PGI / Intel) Hannes Barsch (Wed Oct 26 2005 - 00:54:36 PDT)
- AMBER: Increase the runtime of Amber benchmarks Imran Khan (Wed Oct 26 2005 - 02:23:10 PDT)
- AMBER: seg fault error in resp Kateryna Miroshnychenko (Wed Oct 26 2005 - 06:24:37 PDT)
- AMBER: xleap, opteron, pgi and segmentation fault. Lars Packschies (Wed Oct 26 2005 - 06:57:40 PDT)
- AMBER: using constraints with QM/MM Jakub Kostal (Wed Oct 26 2005 - 11:58:40 PDT)
- AMBER: Re: restraints xiaoqin huang (Wed Oct 26 2005 - 14:25:03 PDT)
- AMBER: some questions when using ATP du yongchun (Wed Oct 26 2005 - 19:28:44 PDT)
- AMBER: restart file and crd file Lishan Yao (Thu Oct 27 2005 - 06:37:29 PDT)
- AMBER: problems installing amber 7 on a RH Linux 8 machine Marios Constantinou (Thu Oct 27 2005 - 08:28:00 PDT)
- AMBER: Unknown atomtypes in amber Nitin Bhardwaj (Thu Oct 27 2005 - 10:26:49 PDT)
- AMBER: Metals with Amber Anton B. Guliaev (Fri Oct 28 2005 - 10:09:07 PDT)
- AMBER: vdw of h atoms Gustavo Pierdominici Sottile (Fri Oct 28 2005 - 12:16:10 PDT)
- Re: AMBER: Metals with Amber Bill Ross (Fri Oct 28 2005 - 13:56:50 PDT)
- Re: AMBER: vdw of h atoms Bill Ross (Fri Oct 28 2005 - 15:13:59 PDT)
- AMBER: Improper Torsional Parameters Ilyas Yildirim (Fri Oct 28 2005 - 17:59:35 PDT)
- AMBER: rounding in xleap when using saveoff command... Ilyas Yildirim (Fri Oct 28 2005 - 18:26:22 PDT)
- AMBER: amber7.0: F,Br,radius in MMPBSA Yong Xu (Sat Oct 29 2005 - 07:46:00 PDT)
- AMBER: amber7.0: F,Br,radius in MMPBSA Yong Xu (Sat Oct 29 2005 - 07:47:21 PDT)
- AMBER: with two water molecules in active site, how to calculate the free energy of ligand bound to complex? haixiao jin (Sun Oct 30 2005 - 22:27:08 PST)
- AMBER: GBSA simulation problem Guillaume Bollot (Mon Oct 31 2005 - 00:23:26 PST)
- AMBER: tkbc2 Mingfeng Yang (Mon Oct 31 2005 - 14:59:17 PST)
- Last message date: Mon Oct 31 2005 - 23:53:01 PST
- Archived on: Wed Mar 10 2010 - 06:00:26 PST
