Amber Archive Oct 2007 by thread
- Re: AMBER: cyclohexane and decalin on amber Jones de Andrade (Sun Sep 30 2007 - 22:46:44 PDT)
- AMBER: regarding non bonded energy caculations gurpreet singh (Sun Sep 30 2007 - 22:41:47 PDT)
- Re: AMBER: MAXPR san_amber roy (Mon Oct 01 2007 - 01:10:35 PDT)
- AMBER: atomicfluct Andres Palencia (Mon Oct 01 2007 - 11:12:20 PDT)
- AMBER: dihedrals Ed Pate (Mon Oct 01 2007 - 16:07:47 PDT)
- AMBER: constant pH Eddie Men (Tue Oct 02 2007 - 02:45:34 PDT)
- AMBER: Constant pH Eddie Men (Tue Oct 02 2007 - 02:41:31 PDT)
- AMBER: multichain simulations priya priya (Tue Oct 02 2007 - 02:31:26 PDT)
- AMBER: Problems with cpin file Eddie Men (Tue Oct 02 2007 - 05:47:50 PDT)
- RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 Ross Walker (Tue Oct 02 2007 - 19:00:07 PDT)
- AMBER: parameterization for copper Syed Tarique Moin (Wed Oct 03 2007 - 03:45:33 PDT)
- AMBER: 31 integers in the first section of a prmtop file David Cerutti (Wed Oct 03 2007 - 09:58:03 PDT)
- AMBER: PBSA generate snapshots saccenti.cerm.unifi.it (Thu Oct 04 2007 - 02:17:04 PDT)
- AMBER: multi chain simulations priya priya (Thu Oct 04 2007 - 03:30:27 PDT)
- AMBER: binary restart file Myunggi Yi (Thu Oct 04 2007 - 07:49:28 PDT)
- AMBER: Problems with 'make' Hopkins, Robert (Thu Oct 04 2007 - 12:07:42 PDT)
- AMBER: Applying bugfixes in Amber Lili Peng (Thu Oct 04 2007 - 14:28:29 PDT)
- AMBER: generating topology files for PBSA saccenti.cerm.unifi.it (Fri Oct 05 2007 - 02:46:14 PDT)
- Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Anthony Cruz (Fri Oct 05 2007 - 05:44:50 PDT)
- AMBER: PMEMD configuration and scaling Lars.Skjarven.biomed.uib.no (Sat Oct 06 2007 - 04:35:03 PDT)
- AMBER: request for hardware recommendations Parish, Carol (Sat Oct 06 2007 - 08:59:01 PDT)
- AMBER: hey Eduardo Mendez (Sat Oct 06 2007 - 22:19:36 PDT)
- AMBER: PMEMD configuration and scaling Lars.Skjarven.biomed.uib.no (Sun Oct 07 2007 - 03:40:00 PDT)
- AMBER: Resp: "Statistics of the Fitting" Jones de Andrade (Sun Oct 07 2007 - 11:40:04 PDT)
- AMBER: regrading interaction energy calculations gurpreet singh (Sun Oct 07 2007 - 21:52:23 PDT)
- AMBER: Problems compiling Amber9 on IBM-AIX Sampath Koppole (Mon Oct 08 2007 - 04:42:20 PDT)
- AMBER: entropy with ptraj Marius Retegan (Mon Oct 08 2007 - 05:24:36 PDT)
- AMBER: adding extra points to amber - how to? Jones de Andrade (Mon Oct 08 2007 - 09:44:42 PDT)
- AMBER: RE: Amber query !! Ross Walker (Mon Oct 08 2007 - 10:02:36 PDT)
- AMBER: Amber9 installation error on Mandriva 2007 linux Joe Nolan (Mon Oct 08 2007 - 10:07:58 PDT)
- AMBER: Quick QUESTION Eddie Men (Mon Oct 08 2007 - 21:23:49 PDT)
- AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water? David Cerutti (Mon Oct 08 2007 - 22:25:43 PDT)
- AMBER: PMEMD configuration and scaling Lars.Skjarven.biomed.uib.no (Tue Oct 09 2007 - 03:05:37 PDT)
- AMBER: RE: antechamber Ross Walker (Tue Oct 09 2007 - 09:51:57 PDT)
- AMBER: interaction energy calculations gurpreet singh (Tue Oct 09 2007 - 10:06:24 PDT)
- Re: AMBER: follow-up Wenyong Tong (Tue Oct 09 2007 - 13:56:04 PDT)
- AMBER: neb for path between binding sites Holly Freedman (Tue Oct 09 2007 - 14:09:50 PDT)
- AMBER: Thermodynamic Integration with Explicit Solvent Scott Pendley (Tue Oct 09 2007 - 14:38:03 PDT)
- AMBER: error in modified PNA -DNA simulation.. Sharad gupta (Wed Oct 10 2007 - 03:39:07 PDT)
- AMBER: ff99SB and the N- and C- charged terminal residues Nicolas Lux Fawzi (Wed Oct 10 2007 - 09:03:09 PDT)
- AMBER: Error- MM_PBSA calculation vikky 99 (Wed Oct 10 2007 - 10:44:53 PDT)
- AMBER: constant-pH MD with replica exchange Maciej Dlugosz (Wed Oct 10 2007 - 23:38:49 PDT)
- AMBER: Error- MM_PBSA calculation vikky 99 (Thu Oct 11 2007 - 00:28:25 PDT)
- AMBER: BOMB! Eddie Men (Thu Oct 11 2007 - 03:12:49 PDT)
- AMBER: lipid bilayer san_amber roy (Thu Oct 11 2007 - 04:52:42 PDT)
- AMBER: Error- MM_PBSA calculation vikky 99 (Thu Oct 11 2007 - 08:01:23 PDT)
- AMBER: Missing 'yacc' command Hopkins, Robert (Sat Oct 13 2007 - 15:00:00 PDT)
- AMBER: Please Disregard My Last E-mail: Missing 'yacc' command Hopkins, Robert (Sat Oct 13 2007 - 16:04:11 PDT)
- AMBER: error in modified PNA DNA simulation Sharad gupta (Sun Oct 14 2007 - 22:35:13 PDT)
- AMBER: anal calculatons gurpreet singh (Mon Oct 15 2007 - 00:19:33 PDT)
- AMBER: RED III Age.Skjevik.student.uib.no (Mon Oct 15 2007 - 03:06:49 PDT)
- AMBER: using amber for cyclic peptides rebeca.mmb.pcb.ub.es (Mon Oct 15 2007 - 10:23:50 PDT)
- AMBER: Water cap MD error Rima Chaudhuri (Mon Oct 15 2007 - 15:17:07 PDT)
- AMBER: MM_PBSA calcultion- help me varsha rani (Mon Oct 15 2007 - 22:53:14 PDT)
- AMBER: Test fails in Parallel version Amber9 gong wb (Mon Oct 15 2007 - 23:42:45 PDT)
- AMBER: amber9 installation problem Madjid Taghdir (Tue Oct 16 2007 - 01:46:05 PDT)
- AMBER: anal calculation error gurpreet singh (Tue Oct 16 2007 - 10:07:20 PDT)
- AMBER: AMBER 9 - Force Field Options - Question dpandit.brandeis.edu (Tue Oct 16 2007 - 13:41:33 PDT)
- AMBER: anal error gurpreet singh (Wed Oct 17 2007 - 11:14:52 PDT)
- AMBER: error while Running TMD gurpreet singh (Wed Oct 17 2007 - 11:21:18 PDT)
- AMBER: Temperature fluctuation in NPT and NVE ensemble Lei Jia (Wed Oct 17 2007 - 16:46:29 PDT)
- AMBER: anal gurpreet singh (Wed Oct 17 2007 - 21:35:23 PDT)
- AMBER: how to simulate a ligand bound to a residue Jena M (Thu Oct 18 2007 - 06:49:55 PDT)
- AMBER: Simulation died due to lack of disk space Samantha Kaye (Thu Oct 18 2007 - 06:57:57 PDT)
- AMBER: Backbone flexibility/entropy Seth Lilavivat (Thu Oct 18 2007 - 14:47:37 PDT)
- AMBER: FORTRAN code for calculating ENERGY of all the four terms (bonds, angles, dihedrals, nonbanded pairs) of Amber8's sander Jiapu.Zhang.csiro.au (Thu Oct 18 2007 - 16:15:05 PDT)
- AMBER: subroutine ephi !! Sampath Koppole (Fri Oct 19 2007 - 01:08:26 PDT)
- AMBER: mm_pbsa: missing values in ras-raf tutorials merc mertens (Fri Oct 19 2007 - 01:28:09 PDT)
- AMBER: Abnormality in MM-PBSA result msubhamoy.ibab.ac.in (Fri Oct 19 2007 - 08:01:16 PDT)
- AMBER: How to use loadpdbusingseq command to load branched structure? Siang Yip (Fri Oct 19 2007 - 10:21:36 PDT)
- AMBER: question about h bond WANG,YING (Fri Oct 19 2007 - 17:19:36 PDT)
- AMBER: Heat capacity calculations not coming out right David Cerutti (Fri Oct 19 2007 - 19:37:38 PDT)
- AMBER: Interactive Molecular Dynamics with Amber? Marc Baaden (Sat Oct 20 2007 - 15:10:23 PDT)
- AMBER: EVB Calculations Jimmy Heimdal (Sun Oct 21 2007 - 23:30:48 PDT)
- AMBER: Problems loading pdb file including Mg ions Idan Gabdank (Mon Oct 22 2007 - 08:53:12 PDT)
- AMBER: results from TI Holly Freedman (Mon Oct 22 2007 - 09:42:26 PDT)
- AMBER: SASA per residue Evan Kelly (Mon Oct 22 2007 - 09:59:26 PDT)
- AMBER: question about charge of prmtop file WANG,YING (Tue Oct 23 2007 - 07:11:22 PDT)
- AMBER: Beowulf cluster from PSSC Labs Aaron Greenwood (Tue Oct 23 2007 - 09:22:33 PDT)
- AMBER: Portland Group vs. Intel Compilers. Aaron Greenwood (Tue Oct 23 2007 - 10:03:43 PDT)
- Re: AMBER: heme forcefield atom types L. W. Yang (Wed Oct 24 2007 - 09:18:31 PDT)
- AMBER: prepin file format description; pointers on parameterization David Mobley (Wed Oct 24 2007 - 10:52:24 PDT)
- RE: AMBER: heme forcefield atom types Yang, Lee-Wei (Wed Oct 24 2007 - 11:41:29 PDT)
- AMBER: regarding anal calculations gurpreet singh (Wed Oct 24 2007 - 11:50:49 PDT)
- AMBER: hbond analysis output Claire Zerafa (Wed Oct 24 2007 - 12:21:02 PDT)
- AMBER: Pre-requisites for AMBER software Anamika Awasthi (Thu Oct 25 2007 - 05:05:19 PDT)
- AMBER: &dipole input and some questions on using polarizable force fields Seongeun Yang (Thu Oct 25 2007 - 06:11:48 PDT)
- AMBER: problems compiling amber on mac OSX francesco zonta (Thu Oct 25 2007 - 06:50:04 PDT)
- AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua Yang, Lee-Wei (Thu Oct 25 2007 - 07:46:00 PDT)
- AMBER: ANGVE/TORAVE Abi Ghanem josephine (Thu Oct 25 2007 - 08:58:11 PDT)
- AMBER: HG atoms in CYX residues francesco zonta (Fri Oct 26 2007 - 02:45:32 PDT)
- AMBER: Heme and CYS !! Pradipta Bandyopadhyay (Fri Oct 26 2007 - 03:49:47 PDT)
- AMBER: segmentation fault occured doing MD priya priya (Fri Oct 26 2007 - 04:51:31 PDT)
- AMBER: RE: about deoxy- and oxy- heme Yang, Lee-Wei (Sun Oct 28 2007 - 01:52:58 PDT)
- AMBER: How can i calculate generalized order parameters using ptraj. cgji (Sun Oct 28 2007 - 07:59:37 PDT)
- AMBER: replica exchange Geoff Wood (Sun Oct 28 2007 - 09:29:42 PDT)
- AMBER: Amber FF parameters for the Zinc-hydroxammate interaction snoze pa (Sun Oct 28 2007 - 17:59:26 PDT)
- AMBER: calculation of angle between helices Anupam Nath Jha (Sun Oct 28 2007 - 23:06:37 PDT)
- AMBER: The number of the path atoms exceeds MAXPATHATOMNUM VANIA MARIA AMARO CALISTO (Mon Oct 29 2007 - 05:13:01 PDT)
- AMBER: RED-vIII fails Jesper Soerensen (Mon Oct 29 2007 - 07:51:56 PDT)
- AMBER: Getting prmtop and inpcrd Francesco Pietra (Mon Oct 29 2007 - 08:43:44 PDT)
- AMBER: amber with periodic condition Mattia Mori - CERM (Mon Oct 29 2007 - 10:16:14 PDT)
- Re: AMBER: Getting prmtop and inpcrd Bill Ross (Mon Oct 29 2007 - 12:26:16 PDT)
- AMBER: mdfil: Error unknown flag: -p4pg Aaron Greenwood (Mon Oct 29 2007 - 12:38:44 PDT)
- AMBER: AMBER 8: QMMM - molecule fluctuates wildly Seth Lilavivat (Mon Oct 29 2007 - 13:40:06 PDT)
- AMBER: Amber9 parallel installation error (with openMPI) Joe Nolan (Mon Oct 29 2007 - 14:02:10 PDT)
- AMBER: Amber 9 source code permissions (UNCLASSIFIED) Monaghan, Martin (Cont, ARL/CISD) (Mon Oct 29 2007 - 14:30:30 PDT)
- AMBER: anal problem varsha rani (Tue Oct 30 2007 - 04:48:03 PDT)
- AMBER: Amber9 parallel installation error (retry) Joe Nolan (Tue Oct 30 2007 - 11:25:35 PDT)
- AMBER: dihedral angles Jardas sucuriba (Tue Oct 30 2007 - 17:43:10 PDT)
- AMBER: antechamber fails with large molecules VANIA MARIA AMARO CALISTO (Wed Oct 31 2007 - 02:26:14 PDT)
- AMBER: problems visualizing mdcrd in VMD Mattia Mori - CERM (Wed Oct 31 2007 - 04:17:21 PDT)
- AMBER: gibbs problems JAVIER PEREZ (Wed Oct 31 2007 - 04:48:22 PDT)
- AMBER: amber9 parallel compile problem Christopher Jones (Wed Oct 31 2007 - 10:09:32 PDT)
- AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) sanket deshmukh (Wed Oct 31 2007 - 11:57:54 PDT)
- Last message date: Sun Nov 04 2007 - 06:07:19 PST
- Archived on: Fri Nov 15 2024 - 05:53:41 PST
