Amber Archive Mar 2008 by thread
- AMBER: regarding:calculation of b factor using ptraj jani sahil (Sat Mar 01 2008 - 08:10:10 PST)
- AMBER: questions about run MD at different pH Kailee (Mon Mar 03 2008 - 06:51:40 PST)
- AMBER: Writing pressure in md.out file in NVT simulation Sudha Mani Karra (Mon Mar 03 2008 - 10:58:46 PST)
- AMBER: xleap screen output Francesco Pietra (Mon Mar 03 2008 - 13:02:54 PST)
- AMBER: ACS COMP Division awards- deadline this week Carlos Simmerling (Mon Mar 03 2008 - 16:14:03 PST)
- AMBER: Problem running implicit minimization Lili Peng (Mon Mar 03 2008 - 21:10:52 PST)
- AMBER: missing gaff parameters Samuele Giani (Tue Mar 04 2008 - 00:46:38 PST)
- Fwd: Re: AMBER: xleap screen output Francesco Pietra (Tue Mar 04 2008 - 09:33:34 PST)
- Fwd: Re: AMBER: xleap screen output SOLVED Francesco Pietra (Tue Mar 04 2008 - 12:44:15 PST)
- Re: Fwd: Re: AMBER: xleap screen output Bill Ross (Tue Mar 04 2008 - 09:59:58 PST)
- RE: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Mohd Farid Ismail (Tue Mar 04 2008 - 17:09:52 PST)
- AMBER: a question about parameter b in the hyperbolic form of penalty function for RESP fit Ye Mei (Wed Mar 05 2008 - 01:30:50 PST)
- AMBER: Atom types/parameters for chromene anna.schrey.gmx.de (Wed Mar 05 2008 - 01:34:24 PST)
- AMBER: setBox command Vijay Manickam Achari (Wed Mar 05 2008 - 21:20:01 PST)
- AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? Edyta Malolepsza (Thu Mar 06 2008 - 04:23:06 PST)
- AMBER: Steve Seibold (Thu Mar 06 2008 - 10:04:01 PST)
- Re: AMBER: XMGRACE on Linux 64 Bit Bill Ross (Thu Mar 06 2008 - 16:12:51 PST)
- AMBER: Microcannonical MD Reference priya priya (Fri Mar 07 2008 - 05:40:34 PST)
- AMBER: NVE energy and temperature drift Lars Skjærven (Fri Mar 07 2008 - 07:36:48 PST)
- AMBER: Fwd: positive potential energy and large 1-4 EEL Mey Khalili (Fri Mar 07 2008 - 08:54:28 PST)
- AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis James Thomas (Fri Mar 07 2008 - 09:30:58 PST)
- AMBER: RE: Request Ross Walker (Fri Mar 07 2008 - 12:38:25 PST)
- AMBER: reg molecular dynamics Uma R (Fri Mar 07 2008 - 19:17:32 PST)
- AMBER: Negative ligand (Peroxide) Syed Tarique Moin (Sat Mar 08 2008 - 03:36:56 PST)
- AMBER: Compiler issues with Altix450 finke.oakland.edu (Sat Mar 08 2008 - 10:37:25 PST)
- AMBER: Clarification on error message Campbell, Patrick (Sat Mar 08 2008 - 12:09:23 PST)
- AMBER: mmpbsa INSTRNG error? Sergio Wong (Sat Mar 08 2008 - 22:06:44 PST)
- AMBER: Timing analysis on Ranger David LeBard (Sun Mar 09 2008 - 13:06:18 PDT)
- AMBER: Antechamber, net molecular charge gurpreet singh (Sun Mar 09 2008 - 21:51:58 PDT)
- AMBER: Benchmarks on Fujitsu PrimePower 2500? Craig Gough (Sun Mar 09 2008 - 22:36:28 PDT)
- Fwd: AMBER: Negative ligand (Peroxide) Syed Tarique Moin (Sun Mar 09 2008 - 22:59:43 PDT)
- AMBER: writing out a distance between two atoms in sander Vlad Cojocaru (Mon Mar 10 2008 - 06:33:55 PDT)
- AMBER: problem with antech amber Madjid Taghdir (Mon Mar 10 2008 - 08:07:16 PDT)
- AMBER: output effective Born radii Holly Freedman (Mon Mar 10 2008 - 15:57:06 PDT)
- AMBER: Re: Amber: parameters for Silicon Scott Brozell (Mon Mar 10 2008 - 16:57:29 PDT)
- Re: AMBER: AMBER install problem David A. Case (Mon Mar 10 2008 - 17:50:30 PDT)
- AMBER: SMD using amber ChengZhong Zhang (Mon Mar 10 2008 - 18:54:23 PDT)
- AMBER: convert AMBER format input files into DL_POLY format input files? Kefa Lu (Tue Mar 11 2008 - 01:27:23 PDT)
- AMBER: solvate with methanol san_amber roy (Tue Mar 11 2008 - 02:23:40 PDT)
- AMBER: Adding New Parameters and Modifying Existing Parameters serhanyigen.mail.ege.edu.tr (Tue Mar 11 2008 - 04:51:18 PDT)
- AMBER: SPARC benchmarks (was re Fujitsu PRIMEPOWER) Atro Tossavainen (Tue Mar 11 2008 - 07:33:33 PDT)
- AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 David Rangel (Tue Mar 11 2008 - 20:30:14 PDT)
- AMBER: lastrst problem san_amber roy (Wed Mar 12 2008 - 08:07:23 PDT)
- AMBER: ptraj and non-bonded contacts Samuel Genheden (a03samge) (Wed Mar 12 2008 - 09:34:44 PDT)
- AMBER: study of protein stability in different ion using AMBER Prem Prakash Pathak (Wed Mar 12 2008 - 23:20:31 PDT)
- AMBER: distance restraint gurpreet singh (Thu Mar 13 2008 - 04:28:28 PDT)
- AMBER: [success] problem compiling Amber9 on Bull Linux Yannick Monclin (Thu Mar 13 2008 - 04:56:48 PDT)
- AMBER: Energy calculation and replica exchange in Amber9 Li Dawei (Thu Mar 13 2008 - 06:50:49 PDT)
- AMBER: can't make antechamber work for regular nucleotides Mey Khalili (Thu Mar 13 2008 - 07:03:45 PDT)
- AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Thu Mar 13 2008 - 07:54:03 PDT)
- AMBER: Temperature Range For REMD tushar garud (Thu Mar 13 2008 - 08:20:02 PDT)
- AMBER: implicit energy calculations rebeca.mmb.pcb.ub.es (Thu Mar 13 2008 - 09:26:43 PDT)
- AMBER: force field oguz gurbulak (Thu Mar 13 2008 - 15:00:58 PDT)
- AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ) Lwin, ThuZar (Thu Mar 13 2008 - 17:13:57 PDT)
- AMBER: How to calculate deformability by PTRAJ ? sychen (Thu Mar 13 2008 - 18:44:36 PDT)
- AMBER: Torsion potential in GAFF / "statistic value of parm94" Alexander Metz (Fri Mar 14 2008 - 05:53:10 PDT)
- AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ). Lwin, ThuZar (Fri Mar 14 2008 - 08:32:25 PDT)
- AMBER: Heating POL3 Box Troubles Paul Johns (Fri Mar 14 2008 - 11:44:44 PDT)
- AMBER: Negative ligand Syed Tarique Moin (Sat Mar 15 2008 - 02:12:09 PDT)
- AMBER: mm_pbsa positive ELE Qi Yan (Mon Mar 17 2008 - 11:20:21 PDT)
- AMBER: compiling AMBER9 with bintraj option on AMD64 Vlad Cojocaru (Fri Mar 14 2008 - 10:44:56 PDT)
- AMBER: What's making my system lose total energy? David Cerutti (Mon Mar 17 2008 - 17:20:30 PDT)
- AMBER: a minor bug in RESP Ye Mei (Tue Mar 18 2008 - 00:05:34 PDT)
- AMBER: problem with distance restrain aneesh cna (Tue Mar 18 2008 - 03:16:09 PDT)
- AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 07:09:34 PDT)
- AMBER: Problems with neglected restaints anna.schrey.gmx.de (Tue Mar 18 2008 - 09:40:20 PDT)
- AMBER: Inquiry on analyzing the amplitude from nmdout results James Thomas (Wed Mar 19 2008 - 09:09:05 PDT)
- AMBER: Amber9 Installation Problem trudy.uoguelph.ca (Wed Mar 19 2008 - 09:28:35 PDT)
- AMBER: MNDO parameters for Mg+2 E.M. (Wed Mar 19 2008 - 10:28:09 PDT)
- AMBER: standard residues Holly Freedman (Wed Mar 19 2008 - 13:03:02 PDT)
- AMBER: Water Topology Ivelin Georgiev (Wed Mar 19 2008 - 21:12:28 PDT)
- AMBER: potential of mean force: Unit of PMF energies and min path Catein Catherine (Wed Mar 19 2008 - 22:26:43 PDT)
- AMBER: Happy holi Bertrand P. S. Russell (Thu Mar 20 2008 - 02:03:22 PDT)
- AMBER: problem with distance restraints aneesh cna (Thu Mar 20 2008 - 03:13:31 PDT)
- AMBER: Charge scheme for simulating protonated adenine prateeksha s (Thu Mar 20 2008 - 23:58:19 PDT)
- AMBER: equilibration of peptide tushar garud (Fri Mar 21 2008 - 21:02:25 PDT)
- AMBER: cntrl namelist error Campbell, Patrick (Sat Mar 22 2008 - 08:40:16 PDT)
- AMBER: RE: Force Field Parameterizing Shultz, Jack (Mon Mar 24 2008 - 08:31:32 PDT)
- AMBER: hybrid remd imaging Geoff Wood (Mon Mar 24 2008 - 08:51:51 PDT)
- AMBER: Nmode segmentation fault James Thomas (Tue Mar 25 2008 - 04:53:21 PDT)
- AMBER: help regarding warning message snoze pa (Tue Mar 25 2008 - 09:17:43 PDT)
- AMBER: anion and cation simulaton gurpreet singh (Tue Mar 25 2008 - 09:22:29 PDT)
- Re: AMBER: addions and addions2 Bill Ross (Tue Mar 25 2008 - 10:34:52 PDT)
- AMBER: Convert dcd to mdcrd Seth Lilavivat (Tue Mar 25 2008 - 11:13:22 PDT)
- AMBER: umbrella sampling for proton transfer cniu.ualberta.ca (Tue Mar 25 2008 - 17:30:33 PDT)
- AMBER: NTR Restraints Daniel Smith (Tue Mar 25 2008 - 18:17:27 PDT)
- AMBER: OPLS force field aneesh cna (Wed Mar 26 2008 - 08:48:19 PDT)
- AMBER: mm-pbsa multiple trajectory approach? Seth Lilavivat (Wed Mar 26 2008 - 10:32:54 PDT)
- AMBER: residual dipolar couplings - alignment tensor energy Douglas Kojetin (Wed Mar 26 2008 - 12:46:48 PDT)
- AMBER: RMSD of two different molecules JunJun Liu (Wed Mar 26 2008 - 13:35:32 PDT)
- AMBER: how to link two different atoms in xLeap snoze pa (Wed Mar 26 2008 - 13:56:12 PDT)
- AMBER: Error with a binary restart file Kijeong Kwac (Wed Mar 26 2008 - 16:07:51 PDT)
- AMBER: PF6 parameters aneesh cna (Wed Mar 26 2008 - 21:43:58 PDT)
- AMBER: Error- MM_PBSA calculation vikky 99 (Thu Mar 27 2008 - 01:47:53 PDT)
- AMBER: FW: MD run time inquiry Campbell, Patrick (Thu Mar 27 2008 - 03:13:00 PDT)
- AMBER: Protein rotating out of box Lars Skjærven (Thu Mar 27 2008 - 14:34:48 PDT)
- AMBER: measuring contacts: error "glibc detected" rebeca.mmb.pcb.ub.es (Fri Mar 28 2008 - 05:26:42 PDT)
- AMBER: GAFF Eric Germaneau (Fri Mar 28 2008 - 05:38:41 PDT)
- AMBER: REMD simulation error Guillaume Renvez (Fri Mar 28 2008 - 07:01:20 PDT)
- AMBER: problem with nmod yuri pomè (Fri Mar 28 2008 - 09:42:54 PDT)
- AMBER: AMBER 9 testing Taufik Al-Sarraj (Fri Mar 28 2008 - 17:18:30 PDT)
- AMBER: meet problem in adding ions and waterbox Qiang Li (Sat Mar 29 2008 - 22:43:54 PDT)
- AMBER: Regarding SHAKE gurpreet singh (Sun Mar 30 2008 - 03:38:48 PDT)
- AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water Markus Kaukonen (Sun Mar 30 2008 - 23:34:48 PDT)
- AMBER: Free energy landscape? HOWTO? Yi-Ming Cheng (Mon Mar 31 2008 - 01:12:05 PDT)
- AMBER: TI: perturbation method fatima.chami.durham.ac.uk (Mon Mar 31 2008 - 01:40:40 PDT)
- AMBER: Select specific residues (leap) Marta Rossini (Mon Mar 31 2008 - 02:28:31 PDT)
- AMBER: energy problems in simulation with restraints Daniel Cappel (Mon Mar 31 2008 - 02:39:13 PDT)
- AMBER: installation amber9 Geoff Wood (Mon Mar 31 2008 - 04:02:01 PDT)
- AMBER: multiple dihedral restraints using group mkseo (Mon Mar 31 2008 - 10:11:30 PDT)
- AMBER: memory limitation of Amber 9 yavuzturkm.prc.boun.edu.tr (Mon Mar 31 2008 - 11:49:40 PDT)
- AMBER: nmode James Thomas (Mon Mar 31 2008 - 11:48:43 PDT)
- AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Mon Mar 31 2008 - 12:45:20 PDT)
- Last message date: Fri Apr 18 2008 - 21:15:44 PDT
- Archived on: Wed Dec 25 2024 - 05:53:41 PST
