AMBER Archive (2005) - Feb 2005 By ThreadMost recent messages
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Starting: Tue Feb 01 2005 - 04:56:21 CST
Ending: Mon Feb 28 2005 - 16:42:21 CST
- AMBER: vacuum bubbles in system equilibration Marie-Pierre Durrieu (Tue Feb 01 2005 - 04:56:21 CST)
- AMBER: Carnal in Amber8 Vlad Cojocaru (Tue Feb 01 2005 - 10:11:09 CST)
- AMBER: Multiple dihedral restraints Joseph Fernandez (Tue Feb 01 2005 - 11:29:40 CST)
- AMBER: Redhat Enterprise Linux Beale, John (Tue Feb 01 2005 - 11:49:20 CST)
- Re: AMBER: Carnal in Amber8 Bill Ross (Tue Feb 01 2005 - 13:47:15 CST)
- AMBER: doubts with a new aminoacid Gustavo Pierdominici Sottile (Tue Feb 01 2005 - 14:28:52 CST)
- AMBER: External Electric Field Brandon Tefft (Tue Feb 01 2005 - 15:30:22 CST)
- AMBER: sander segmentation fault Xin Wang (Tue Feb 01 2005 - 16:15:12 CST)
- AMBER: xleap: different distance results from "check" command in xleap Woojin Lee (Tue Feb 01 2005 - 23:54:14 CST)
- AMBER: Compilation problem at dual processor linux ! Pradipta Bandyopadhyay (Wed Feb 02 2005 - 06:32:52 CST)
- AMBER: change of prmtop file Gustavo Pierdominici Sottile (Wed Feb 02 2005 - 09:43:34 CST)
- AMBER: xleap MOVE and .lib file Stern, Julie (Wed Feb 02 2005 - 11:01:55 CST)
- AMBER: amber 8 system requirements dkohen_at_carleton.edu (Wed Feb 02 2005 - 12:28:48 CST)
- AMBER: gaff frcmod file for TI calculation Eric Hu (Wed Feb 02 2005 - 17:50:00 CST)
- AMBER: question about tleap load pdb file xiaowen (Wed Feb 02 2005 - 21:19:19 CST)
- AMBER: protonate and input conversion error Stern, Julie (Thu Feb 03 2005 - 10:48:20 CST)
- AMBER: DNA melting free energy calculation lei jia (Thu Feb 03 2005 - 18:39:57 CST)
- AMBER: unnatural ligand Eric Hu (Thu Feb 03 2005 - 21:37:41 CST)
- AMBER: clusters Germán Sciaini (Fri Feb 04 2005 - 06:36:48 CST)
- AMBER: tleap load pdb file xiaowen (Fri Feb 04 2005 - 09:44:17 CST)
- AMBER: tleap load pdb file xiaowen (Fri Feb 04 2005 - 15:18:09 CST)
- AMBER: Antechamber/formatting question Kara Di Giorgio (Fri Feb 04 2005 - 17:05:18 CST)
- AMBER: huge bond distances in new residue Stern, Julie (Fri Feb 04 2005 - 17:48:14 CST)
- AMBER: trajectory of minimization Stern, Julie (Fri Feb 04 2005 - 17:49:17 CST)
- AMBER: Is droplet boundary condition option possible ? Soo (Sat Feb 05 2005 - 00:18:36 CST)
- AMBER: loading pdb in leap to create parmeter files mrbroad_at_ilstu.edu (Sat Feb 05 2005 - 15:24:04 CST)
- AMBER: Tutorial Request Kara Di Giorgio (Sun Feb 06 2005 - 11:01:15 CST)
- AMBER: inconsistent ordering in an improper dihedral of TRP Sanghyun Park (Sun Feb 06 2005 - 22:38:03 CST)
- AMBER: correlation along PCA modes Vlad Cojocaru (Mon Feb 07 2005 - 05:35:44 CST)
- Re: AMBER: Creating an input file for GRASP using AMBER 8 Bill Ross (Mon Feb 07 2005 - 13:40:33 CST)
- AMBER: problem in writing Gustavo Pierdominici Sottile (Mon Feb 07 2005 - 13:59:49 CST)
- AMBER: How to calculate RESTRAINT value Mayumi Haga (Mon Feb 07 2005 - 22:09:25 CST)
- AMBER: dynamics error S.Sundar Raman (Tue Feb 08 2005 - 05:10:19 CST)
- AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel Fabien Cailliez (Tue Feb 08 2005 - 11:16:51 CST)
- AMBER: problem in minimization Gustavo Pierdominici Sottile (Tue Feb 08 2005 - 12:31:17 CST)
- AMBER: Minimization Beale, John (Tue Feb 08 2005 - 13:30:52 CST)
- AMBER: Linux Enterprise Beale, John (Tue Feb 08 2005 - 13:39:54 CST)
- AMBER: Amber8 installation test possible failures Joe Nolan (Tue Feb 08 2005 - 13:55:39 CST)
- AMBER: leap bond angle building Stern, Julie (Tue Feb 08 2005 - 17:44:39 CST)
- Re: AMBER: leap bond angle building Bill Ross (Tue Feb 08 2005 - 18:00:12 CST)
- AMBER: minimize a ptraj average pdb structure Eric Hu (Tue Feb 08 2005 - 19:48:26 CST)
- AMBER: energy plot in minimization Gustavo Pierdominici Sottile (Wed Feb 09 2005 - 11:36:25 CST)
- AMBER: question about mm_gbsa output file michael chen (Wed Feb 09 2005 - 12:10:06 CST)
- AMBER: Convert to Pdb Beale, John (Wed Feb 09 2005 - 13:03:27 CST)
- AMBER: minimization.out Gustavo Pierdominici Sottile (Wed Feb 09 2005 - 13:32:01 CST)
- AMBER: DIVCON optimization Kara Di Giorgio (Wed Feb 09 2005 - 13:46:03 CST)
- AMBER: Can REM be used as multiple normal sander jobs on parallel machine qlu_at_notes.cc.sunysb.edu (Wed Feb 09 2005 - 17:15:59 CST)
- AMBER: desc NEWRES and blank unit type Stern, Julie (Wed Feb 09 2005 - 20:07:00 CST)
- AMBER: Another question about surface area calculation michael chen (Thu Feb 10 2005 - 00:26:00 CST)
- AMBER: question about surface area to GBsurf calculation michael chen (Thu Feb 10 2005 - 00:20:58 CST)
- AMBER: Poisson Boltzmann dynamics error Rachel Burdge (Thu Feb 10 2005 - 10:04:55 CST)
- AMBER: Protonate state of ARG and LYS. Liu, Jingyuan (Thu Feb 10 2005 - 15:56:39 CST)
- AMBER: How to converts a binary mdcrd file thanyarat Udom (Fri Feb 11 2005 - 01:02:21 CST)
- AMBER: How to converts a binary mdcrd file thanyarat Udom (Fri Feb 11 2005 - 02:00:10 CST)
- AMBER: Cu++ and RED Cenk Andac (Fri Feb 11 2005 - 03:46:13 CST)
- AMBER: too much vacuum in the box created by Leap Marie-Pierre Durrieu (Fri Feb 11 2005 - 06:53:35 CST)
- AMBER: ptraj error and min problems Gustavo Pierdominici Sottile (Fri Feb 11 2005 - 08:54:23 CST)
- AMBER: archive Gustavo Pierdominici Sottile (Fri Feb 11 2005 - 08:58:33 CST)
- AMBER: reverse TI charge perturbation Eric Hu (Fri Feb 11 2005 - 19:59:10 CST)
- AMBER: S.Sundar Raman (Mon Feb 14 2005 - 03:03:27 CST)
- AMBER:how to analyse trajectory files S.Sundar Raman (Mon Feb 14 2005 - 03:17:39 CST)
- AMBER: vlimit Gustavo Pierdominici Sottile (Mon Feb 14 2005 - 06:23:31 CST)
- AMBER: AMBER 8 : Water cap problem Guillaume Bollot (Mon Feb 14 2005 - 07:14:20 CST)
- AMBER: constrains Gustavo Pierdominici Sottile (Mon Feb 14 2005 - 08:53:18 CST)
- AMBER: Restart Problem opitz_at_che.udel.edu (Mon Feb 14 2005 - 13:12:54 CST)
- AMBER: Mainchain example needed Kara Wald (Mon Feb 14 2005 - 15:43:06 CST)
- AMBER: running shell scripts in tleap? Cenk Andac (Mon Feb 14 2005 - 16:23:44 CST)
- AMBER: Topology Format Amber 8 Stuart Murdock (Tue Feb 15 2005 - 06:00:56 CST)
- AMBER: problems with running sander in parallel on linux Piotr Cieplak (Tue Feb 15 2005 - 12:28:02 CST)
- AMBER: blows up Gustavo Pierdominici Sottile (Tue Feb 15 2005 - 13:11:43 CST)
- AMBER: check in leap Gustavo Pierdominici Sottile (Tue Feb 15 2005 - 13:34:21 CST)
- AMBER: Cyclic peptide arubin_at_unmc.edu (Tue Feb 15 2005 - 15:12:28 CST)
- AMBER: PDB conversion to gzmat using antechamber Scott Pendley (Tue Feb 15 2005 - 17:32:21 CST)
- AMBER: EWALD and belly not strictly correct Stern, Julie (Tue Feb 15 2005 - 23:41:49 CST)
- AMBER: Why I couldnt used carnal for analyzed RMSD ? thanyarat Udom (Wed Feb 16 2005 - 03:28:17 CST)
- AMBER: Gustavo Pierdominici Sottile (Wed Feb 16 2005 - 06:22:59 CST)
- AMBER: rms Gustavo Pierdominici Sottile (Wed Feb 16 2005 - 07:14:50 CST)
- AMBER: Beale, John (Wed Feb 16 2005 - 07:42:26 CST)
- AMBER: Phi-Psi-Energy plot L Jin (Wed Feb 16 2005 - 09:45:18 CST)
- AMBER: generate charmm paramater file from amber parm file HL Eastwood (Wed Feb 16 2005 - 11:19:56 CST)
- Re: AMBER: Why I couldnt used carnal for analyzed RMSD ? Bill Ross (Wed Feb 16 2005 - 12:19:30 CST)
- AMBER: Amber7 nmropt Markus W. Germann (Wed Feb 16 2005 - 15:09:08 CST)
- AMBER: installation of amber 8 on windows anshul_at_imtech.res.in (Thu Feb 17 2005 - 14:17:11 CST)
- AMBER: Re: pmemd problems Robert Duke (Thu Feb 17 2005 - 09:15:33 CST)
- AMBER: rotameric populations? Cenk Andac (Thu Feb 17 2005 - 09:15:05 CST)
- AMBER: moil-view Beale, John (Thu Feb 17 2005 - 09:56:30 CST)
- AMBER: Antechamber help needed Kara Di Giorgio (Thu Feb 17 2005 - 11:24:34 CST)
- AMBER: Moil view trajectory clusters Austin B. Yongye (Thu Feb 17 2005 - 11:36:15 CST)
- AMBER: problem with ptraj and randomizeions Fabien Cailliez (Thu Feb 17 2005 - 11:56:24 CST)
- AMBER: PSC Summer Workshop: Modeling Proteins and Nucleic Acids with AMBER, VMD and the MMTSB Toolkit Troy Wymore (Thu Feb 17 2005 - 13:00:36 CST)
- AMBER: amber8 and moil-view Lihua Wang (Thu Feb 17 2005 - 13:26:32 CST)
- AMBER: Amber8 Solaris installation failure Joe Nolan (Thu Feb 17 2005 - 14:27:12 CST)
- AMBER: sander errors with atom restraints on ia64 Rachel Burdge (Thu Feb 17 2005 - 15:46:04 CST)
- AMBER: leap saveamberparm chain types response Stern, Julie (Thu Feb 17 2005 - 17:16:50 CST)
- AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) Greg Recine (Thu Feb 17 2005 - 18:23:01 CST)
- Re: AMBER: leap saveamberparm chain types response Bill Ross (Thu Feb 17 2005 - 19:15:20 CST)
- AMBER: GB solvation and "boxed" environment simulation Soo (Thu Feb 17 2005 - 23:32:38 CST)
- AMBER: molecule blowing apart during equilibration Stern, Julie (Fri Feb 18 2005 - 01:12:16 CST)
- AMBER: ptraj Gustavo Pierdominici Sottile (Fri Feb 18 2005 - 08:58:37 CST)
- AMBER: XMGR Beale, John (Fri Feb 18 2005 - 12:20:44 CST)
- AMBER: DNA Tutorial Dwayne Hoobler (Fri Feb 18 2005 - 17:07:34 CST)
- AMBER: Amber: sander error segmentation fault. S.Sundar Raman (Sat Feb 19 2005 - 00:03:50 CST)
- AMBER: ptraj for RDF calculations Javier Perez Miron (Sat Feb 19 2005 - 10:47:02 CST)
- AMBER: simulation with explicit water molecules Ye MEI (Sat Feb 19 2005 - 21:24:48 CST)
- AMBER: (no subject) yen li (Sun Feb 20 2005 - 12:16:32 CST)
- AMBER: AIX problem Mayumi Haga (Sun Feb 20 2005 - 23:17:29 CST)
- AMBER: ptraj for RDF calculations Javier Perez Miron (Mon Feb 21 2005 - 02:42:33 CST)
- AMBER: Amber 8 with lam compilation problem m m (Mon Feb 21 2005 - 02:55:49 CST)
- AMBER: problem with protein minimization yen li (Mon Feb 21 2005 - 03:12:02 CST)
- AMBER: separate solvent-solvent and solvent-solute interaction Ye MEI (Mon Feb 21 2005 - 06:44:22 CST)
- AMBER: Formatting Questions Kara Di Giorgio (Mon Feb 21 2005 - 13:09:44 CST)
- AMBER: Free energy extimate for the same structure but different conformers claudio (Mon Feb 21 2005 - 14:56:10 CST)
- AMBER: ptraj problem Mayumi Haga (Tue Feb 22 2005 - 03:38:43 CST)
- AMBER: restraint only for Z cartegian coordinate? Jaroslav Hanus (Tue Feb 22 2005 - 09:40:58 CST)
- AMBER: Restraint of atoms during minimization L Jin (Tue Feb 22 2005 - 10:17:05 CST)
- AMBER: dihedral driver? Beale, John (Tue Feb 22 2005 - 10:26:26 CST)
- AMBER: vlimit exceeded and temperature blow up Stern, Julie (Tue Feb 22 2005 - 10:36:05 CST)
- AMBER: MPI for sander8 S. Frank Yan (Tue Feb 22 2005 - 11:04:56 CST)
- AMBER: ptraj8: trajectory windows Anselm Horn (Tue Feb 22 2005 - 11:16:13 CST)
- AMBER: lastrst Stern, Julie (Tue Feb 22 2005 - 17:06:24 CST)
- AMBER: minimizing structures before MM-PBSA? scopio (Tue Feb 22 2005 - 19:23:37 CST)
- AMBER: lastrst Stern, Julie (Tue Feb 22 2005 - 19:21:00 CST)
- AMBER: convert one functional group to another with TI Eric Hu (Tue Feb 22 2005 - 19:29:42 CST)
- AMBER: total energy of solvation Holly Freedman (Tue Feb 22 2005 - 22:05:36 CST)
- AMBER: size of solventbox mathew k varghese (Tue Feb 22 2005 - 22:07:00 CST)
- AMBER: mpirun sander8 problem S. Frank Yan (Wed Feb 23 2005 - 01:13:34 CST)
- AMBER: RE:Amber 8 with lam compilation problem Maciej KA (Wed Feb 23 2005 - 02:07:37 CST)
- Re: AMBER: lastrst Stern, Julie (Wed Feb 23 2005 - 15:03:57 CST)
- AMBER: classes Gustavo Pierdominici Sottile (Wed Feb 23 2005 - 15:00:47 CST)
- AMBER: solvateOct method Cameron Mura (Wed Feb 23 2005 - 20:26:19 CST)
- Re: AMBER: Use of ibelly with nmode analysis marti (Thu Feb 24 2005 - 05:47:28 CST)
- AMBER: How to build dynamics input for guanine with tleap ? Maciej (Thu Feb 24 2005 - 07:44:37 CST)
- AMBER: Joining residues/units Bogos Agianian (Thu Feb 24 2005 - 08:58:55 CST)
- AMBER: cross-correlation Xin Hu (Thu Feb 24 2005 - 10:40:54 CST)
- AMBER: ambpdb radii Harianto (Thu Feb 24 2005 - 13:24:39 CST)
- AMBER: units describing projection onto modes Vlad Cojocaru (Thu Feb 24 2005 - 12:40:18 CST)
- AMBER: correlation Gustavo Pierdominici Sottile (Thu Feb 24 2005 - 13:48:50 CST)
- AMBER: pmemd + pgi 5.1 + ntr = 1 Peter Varnai (Thu Feb 24 2005 - 16:25:04 CST)
- AMBER: My last posting Robert Duke (Thu Feb 24 2005 - 22:15:08 CST)
- AMBER: compile amber8 on RHEL4 HuiZhe Li (Fri Feb 25 2005 - 01:59:02 CST)
- AMBER: nmode entropy calculations in MMPBSA Fabien Cailliez (Fri Feb 25 2005 - 04:20:23 CST)
- AMBER: vlimit Gustavo Pierdominici Sottile (Fri Feb 25 2005 - 06:45:35 CST)
- AMBER: make test.lmod error yuann (Fri Feb 25 2005 - 10:45:11 CST)
- AMBER: setBox buffer in leap Stern, Julie (Fri Feb 25 2005 - 12:43:19 CST)
- AMBER: problem with solvateBox ReichertD_at_mir.wustl.edu (Fri Feb 25 2005 - 14:38:51 CST)
- AMBER: Austin B. Yongye (Fri Feb 25 2005 - 15:43:56 CST)
- AMBER: ico(i)=-1? Xiao He (Fri Feb 25 2005 - 21:49:46 CST)
- AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem praveena moldy (Sun Feb 27 2005 - 23:36:36 CST)
- AMBER: GBSA calculation Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Mon Feb 28 2005 - 04:59:23 CST)
- AMBER: creating a new residue Amber admin (Mon Feb 28 2005 - 10:44:59 CST)
Last message date: Sat Dec 31 2005 - 12:51:27 CST
Archived on: Sat Dec 31 2005 - 12:51:45 CST
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