AMBER Archive (2008) - Mar 2008 By ThreadMost recent messages
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Starting: Sat Mar 01 2008 - 10:10:10 CST
Ending: Mon Mar 31 2008 - 15:40:52 CDT
- AMBER: regarding:calculation of b factor using ptraj jani sahil (Sat Mar 01 2008 - 10:10:10 CST)
- AMBER: questions about run MD at different pH Kailee (Mon Mar 03 2008 - 08:51:40 CST)
- AMBER: Writing pressure in md.out file in NVT simulation Sudha Mani Karra (Mon Mar 03 2008 - 12:58:46 CST)
- AMBER: xleap screen output Francesco Pietra (Mon Mar 03 2008 - 15:02:54 CST)
- AMBER: ACS COMP Division awards- deadline this week Carlos Simmerling (Mon Mar 03 2008 - 18:14:03 CST)
- AMBER: Problem running implicit minimization Lili Peng (Mon Mar 03 2008 - 23:10:52 CST)
- AMBER: missing gaff parameters Samuele Giani (Tue Mar 04 2008 - 02:46:38 CST)
- Fwd: Re: AMBER: xleap screen output Francesco Pietra (Tue Mar 04 2008 - 11:33:34 CST)
- Fwd: Re: AMBER: xleap screen output SOLVED Francesco Pietra (Tue Mar 04 2008 - 14:44:15 CST)
- Re: Fwd: Re: AMBER: xleap screen output Bill Ross (Tue Mar 04 2008 - 11:59:58 CST)
- AMBER: a question about parameter b in the hyperbolic form of penalty function for RESP fit Ye Mei (Wed Mar 05 2008 - 03:30:50 CST)
- AMBER: Atom types/parameters for chromene anna.schrey_at_gmx.de (Wed Mar 05 2008 - 03:34:24 CST)
- AMBER: setBox command Vijay Manickam Achari (Wed Mar 05 2008 - 23:20:01 CST)
- AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? Edyta Malolepsza (Thu Mar 06 2008 - 06:23:06 CST)
- AMBER: Steve Seibold (Thu Mar 06 2008 - 12:04:01 CST)
- Re: AMBER: XMGRACE on Linux 64 Bit Bill Ross (Thu Mar 06 2008 - 18:12:51 CST)
- AMBER: Microcannonical MD Reference priya priya (Fri Mar 07 2008 - 07:40:34 CST)
- AMBER: NVE energy and temperature drift Lars Skjærven (Fri Mar 07 2008 - 09:36:48 CST)
- AMBER: Fwd: positive potential energy and large 1-4 EEL Mey Khalili (Fri Mar 07 2008 - 10:54:28 CST)
- AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis James Thomas (Fri Mar 07 2008 - 11:30:58 CST)
- AMBER: AMBER install problem Kijeong Kwac (Fri Mar 07 2008 - 12:12:08 CST)
- AMBER: RE: Request Ross Walker (Fri Mar 07 2008 - 14:38:25 CST)
- AMBER: reg molecular dynamics Uma R (Fri Mar 07 2008 - 21:17:32 CST)
- AMBER: Negative ligand (Peroxide) Syed Tarique Moin (Sat Mar 08 2008 - 05:36:56 CST)
- AMBER: Compiler issues with Altix450 finke_at_oakland.edu (Sat Mar 08 2008 - 12:37:25 CST)
- AMBER: Clarification on error message Campbell, Patrick (Sat Mar 08 2008 - 14:09:23 CST)
- AMBER: mmpbsa INSTRNG error? Sergio Wong (Sun Mar 09 2008 - 00:06:44 CST)
- AMBER: Timing analysis on Ranger David LeBard (Sun Mar 09 2008 - 15:06:18 CDT)
- AMBER: Antechamber, net molecular charge gurpreet singh (Sun Mar 09 2008 - 23:51:58 CDT)
- AMBER: Benchmarks on Fujitsu PrimePower 2500? Craig Gough (Mon Mar 10 2008 - 00:36:28 CDT)
- Fwd: AMBER: Negative ligand (Peroxide) Syed Tarique Moin (Mon Mar 10 2008 - 00:59:43 CDT)
- AMBER: writing out a distance between two atoms in sander Vlad Cojocaru (Mon Mar 10 2008 - 08:33:55 CDT)
- AMBER: problem with antech amber Madjid Taghdir (Mon Mar 10 2008 - 10:07:16 CDT)
- AMBER: output effective Born radii Holly Freedman (Mon Mar 10 2008 - 17:57:06 CDT)
- AMBER: Re: Amber: parameters for Silicon Scott Brozell (Mon Mar 10 2008 - 18:57:29 CDT)
- AMBER: SMD using amber ChengZhong Zhang (Mon Mar 10 2008 - 20:54:23 CDT)
- AMBER: convert AMBER format input files into DL_POLY format input files? Kefa Lu (Tue Mar 11 2008 - 03:27:23 CDT)
- AMBER: solvate with methanol san_amber roy (Tue Mar 11 2008 - 04:23:40 CDT)
- AMBER: Adding New Parameters and Modifying Existing Parameters serhanyigen_at_mail.ege.edu.tr (Tue Mar 11 2008 - 06:51:18 CDT)
- AMBER: SPARC benchmarks (was re Fujitsu PRIMEPOWER) Atro Tossavainen (Tue Mar 11 2008 - 09:33:33 CDT)
- AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 David Rangel (Tue Mar 11 2008 - 22:30:14 CDT)
- AMBER: lastrst problem san_amber roy (Wed Mar 12 2008 - 10:07:23 CDT)
- AMBER: ptraj and non-bonded contacts Samuel Genheden (a03samge) (Wed Mar 12 2008 - 11:34:44 CDT)
- AMBER: study of protein stability in different ion using AMBER Prem Prakash Pathak (Thu Mar 13 2008 - 01:20:31 CDT)
- AMBER: distance restraint gurpreet singh (Thu Mar 13 2008 - 06:28:28 CDT)
- AMBER: [success] problem compiling Amber9 on Bull Linux Yannick Monclin (Thu Mar 13 2008 - 06:56:48 CDT)
- AMBER: Energy calculation and replica exchange in Amber9 Li Dawei (Thu Mar 13 2008 - 08:50:49 CDT)
- AMBER: can't make antechamber work for regular nucleotides Mey Khalili (Thu Mar 13 2008 - 09:03:45 CDT)
- AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Thu Mar 13 2008 - 09:54:03 CDT)
- AMBER: Temperature Range For REMD tushar garud (Thu Mar 13 2008 - 10:20:02 CDT)
- AMBER: force field oguz gurbulak (Thu Mar 13 2008 - 17:00:58 CDT)
- AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ) Lwin, ThuZar (Thu Mar 13 2008 - 19:13:57 CDT)
- AMBER: How to calculate deformability by PTRAJ ? sychen (Thu Mar 13 2008 - 20:44:36 CDT)
- AMBER: Torsion potential in GAFF / "statistic value of parm94" Alexander Metz (Fri Mar 14 2008 - 07:53:10 CDT)
- AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ). Lwin, ThuZar (Fri Mar 14 2008 - 10:32:25 CDT)
- AMBER: Heating POL3 Box Troubles Paul Johns (Fri Mar 14 2008 - 13:44:44 CDT)
- AMBER: Negative ligand Syed Tarique Moin (Sat Mar 15 2008 - 04:12:09 CDT)
- AMBER: mm_pbsa positive ELE Qi Yan (Mon Mar 17 2008 - 13:20:21 CDT)
- AMBER: compiling AMBER9 with bintraj option on AMD64 Vlad Cojocaru (Fri Mar 14 2008 - 12:44:56 CDT)
- AMBER: What's making my system lose total energy? David Cerutti (Mon Mar 17 2008 - 19:20:30 CDT)
- AMBER: a minor bug in RESP Ye Mei (Tue Mar 18 2008 - 02:05:34 CDT)
- AMBER: problem with distance restrain aneesh cna (Tue Mar 18 2008 - 05:16:09 CDT)
- AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 09:09:34 CDT)
- AMBER: Problems with neglected restaints anna.schrey_at_gmx.de (Tue Mar 18 2008 - 11:40:20 CDT)
- AMBER: Inquiry on analyzing the amplitude from nmdout results James Thomas (Wed Mar 19 2008 - 11:09:05 CDT)
- AMBER: Amber9 Installation Problem trudy_at_uoguelph.ca (Wed Mar 19 2008 - 11:28:35 CDT)
- AMBER: Amber9 Installation Problem trudy_at_uoguelph.ca (Wed Mar 19 2008 - 11:28:35 CDT)
- AMBER: MNDO parameters for Mg+2 E.M. (Wed Mar 19 2008 - 12:28:09 CDT)
- AMBER: standard residues Holly Freedman (Wed Mar 19 2008 - 15:03:02 CDT)
- AMBER: Water Topology Ivelin Georgiev (Wed Mar 19 2008 - 23:12:28 CDT)
- AMBER: potential of mean force: Unit of PMF energies and min path Catein Catherine (Thu Mar 20 2008 - 00:26:43 CDT)
- AMBER: Happy holi Bertrand P. S. Russell (Thu Mar 20 2008 - 04:03:22 CDT)
- AMBER: problem with distance restraints aneesh cna (Thu Mar 20 2008 - 05:13:31 CDT)
- AMBER: Charge scheme for simulating protonated adenine prateeksha s (Fri Mar 21 2008 - 01:58:19 CDT)
- AMBER: equilibration of peptide tushar garud (Fri Mar 21 2008 - 23:02:25 CDT)
- AMBER: cntrl namelist error Campbell, Patrick (Sat Mar 22 2008 - 10:40:16 CDT)
- AMBER: RE: Force Field Parameterizing Shultz, Jack (Mon Mar 24 2008 - 10:31:32 CDT)
- AMBER: hybrid remd imaging Geoff Wood (Mon Mar 24 2008 - 10:51:51 CDT)
- AMBER: Nmode segmentation fault James Thomas (Tue Mar 25 2008 - 06:53:21 CDT)
- AMBER: anion and cation simulaton gurpreet singh (Tue Mar 25 2008 - 11:22:29 CDT)
- AMBER: help regarding warning message snoze pa (Tue Mar 25 2008 - 11:17:43 CDT)
- Re: AMBER: addions and addions2 Bill Ross (Tue Mar 25 2008 - 12:34:52 CDT)
- AMBER: Convert dcd to mdcrd Seth Lilavivat (Tue Mar 25 2008 - 13:13:22 CDT)
- AMBER: umbrella sampling for proton transfer cniu_at_ualberta.ca (Tue Mar 25 2008 - 19:30:33 CDT)
- AMBER: NTR Restraints Daniel Smith (Tue Mar 25 2008 - 20:17:27 CDT)
- AMBER: OPLS force field aneesh cna (Wed Mar 26 2008 - 10:48:19 CDT)
- AMBER: mm-pbsa multiple trajectory approach? Seth Lilavivat (Wed Mar 26 2008 - 12:32:54 CDT)
- AMBER: residual dipolar couplings - alignment tensor energy Douglas Kojetin (Wed Mar 26 2008 - 14:46:48 CDT)
- AMBER: RMSD of two different molecules JunJun Liu (Wed Mar 26 2008 - 15:35:32 CDT)
- AMBER: how to link two different atoms in xLeap snoze pa (Wed Mar 26 2008 - 15:56:12 CDT)
- AMBER: Error with a binary restart file Kijeong Kwac (Wed Mar 26 2008 - 18:07:51 CDT)
- AMBER: PF6 parameters aneesh cna (Wed Mar 26 2008 - 23:43:58 CDT)
- AMBER: Error- MM_PBSA calculation vikky 99 (Thu Mar 27 2008 - 03:47:53 CDT)
- AMBER: FW: MD run time inquiry Campbell, Patrick (Thu Mar 27 2008 - 05:13:00 CDT)
- AMBER: Protein rotating out of box Lars Skjærven (Thu Mar 27 2008 - 16:34:48 CDT)
- AMBER: measuring contacts: error "glibc detected" rebeca_at_mmb.pcb.ub.es (Fri Mar 28 2008 - 07:26:42 CDT)
- AMBER: GAFF Eric Germaneau (Fri Mar 28 2008 - 07:38:41 CDT)
- AMBER: REMD simulation error Guillaume Renvez (Fri Mar 28 2008 - 09:01:20 CDT)
- AMBER: problem with nmod yuri pomè (Fri Mar 28 2008 - 11:42:54 CDT)
- AMBER: meet problem in adding ions and waterbox Qiang Li (Sun Mar 30 2008 - 00:43:54 CDT)
- AMBER: Regarding SHAKE gurpreet singh (Sun Mar 30 2008 - 05:38:48 CDT)
- AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water Markus Kaukonen (Mon Mar 31 2008 - 01:34:48 CDT)
- AMBER: Free energy landscape? HOWTO? Yi-Ming Cheng (Mon Mar 31 2008 - 03:12:05 CDT)
- AMBER: TI: perturbation method fatima.chami_at_durham.ac.uk (Mon Mar 31 2008 - 03:40:40 CDT)
- AMBER: energy problems in simulation with restraints Daniel Cappel (Mon Mar 31 2008 - 04:39:13 CDT)
- AMBER: Select specific residues (leap) Marta Rossini (Mon Mar 31 2008 - 04:28:31 CDT)
- AMBER: installation amber9 Geoff Wood (Mon Mar 31 2008 - 06:02:01 CDT)
- AMBER: multiple dihedral restraints using group mkseo (Mon Mar 31 2008 - 12:11:30 CDT)
- AMBER: memory limitation of Amber 9 yavuzturkm_at_prc.boun.edu.tr (Mon Mar 31 2008 - 13:49:40 CDT)
- AMBER: nmode James Thomas (Mon Mar 31 2008 - 13:48:43 CDT)
- AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Mon Mar 31 2008 - 14:45:20 CDT)
Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:47 CST
341 messages sorted by:
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