Amber Archive Feb 2005 By Thread
- AMBER: amber8 in IBM-SP4 Jiten (Mon Jan 31 2005 - 19:32:28 PST)
- AMBER: N Metyl amino acids Andrew Box (Mon Jan 31 2005 - 21:14:47 PST)
- AMBER: vacuum bubbles in system equilibration Marie-Pierre Durrieu (Tue Feb 01 2005 - 02:56:21 PST)
- Re: AMBER: Problem in ptraj anshul.imtech.res.in (Tue Feb 01 2005 - 14:26:48 PST)
- AMBER: Carnal in Amber8 Vlad Cojocaru (Tue Feb 01 2005 - 08:11:09 PST)
- AMBER: Multiple dihedral restraints Joseph Fernandez (Tue Feb 01 2005 - 09:29:40 PST)
- AMBER: Redhat Enterprise Linux Beale, John (Tue Feb 01 2005 - 09:49:20 PST)
- Re: AMBER: Carnal in Amber8 Bill Ross (Tue Feb 01 2005 - 11:47:15 PST)
- AMBER: doubts with a new aminoacid Gustavo Pierdominici Sottile (Tue Feb 01 2005 - 12:28:52 PST)
- AMBER: External Electric Field Brandon Tefft (Tue Feb 01 2005 - 13:30:22 PST)
- AMBER: sander segmentation fault Xin Wang (Tue Feb 01 2005 - 14:15:12 PST)
- RE: AMBER: gaussian output file Junmei Wang (Tue Feb 01 2005 - 15:03:22 PST)
- AMBER: xleap: different distance results from "check" command in xleap Woojin Lee (Tue Feb 01 2005 - 21:54:14 PST)
- AMBER: Compilation problem at dual processor linux ! Pradipta Bandyopadhyay (Wed Feb 02 2005 - 04:32:52 PST)
- AMBER: change of prmtop file Gustavo Pierdominici Sottile (Wed Feb 02 2005 - 07:43:34 PST)
- AMBER: xleap MOVE and .lib file Stern, Julie (Wed Feb 02 2005 - 09:01:55 PST)
- AMBER: amber 8 system requirements dkohen.carleton.edu (Wed Feb 02 2005 - 10:28:48 PST)
- AMBER: gaff frcmod file for TI calculation Eric Hu (Wed Feb 02 2005 - 15:50:00 PST)
- AMBER: question about tleap load pdb file xiaowen (Wed Feb 02 2005 - 19:19:19 PST)
- AMBER: protonate and input conversion error Stern, Julie (Thu Feb 03 2005 - 08:48:20 PST)
- AMBER: DNA melting free energy calculation lei jia (Thu Feb 03 2005 - 16:39:57 PST)
- AMBER: unnatural ligand Eric Hu (Thu Feb 03 2005 - 19:37:41 PST)
- AMBER: clusters Germán Sciaini (Fri Feb 04 2005 - 04:36:48 PST)
- AMBER: tleap load pdb file xiaowen (Fri Feb 04 2005 - 07:44:17 PST)
- AMBER: tleap load pdb file xiaowen (Fri Feb 04 2005 - 13:18:09 PST)
- AMBER: Antechamber/formatting question Kara Di Giorgio (Fri Feb 04 2005 - 15:05:18 PST)
- AMBER: huge bond distances in new residue Stern, Julie (Fri Feb 04 2005 - 15:48:14 PST)
- AMBER: trajectory of minimization Stern, Julie (Fri Feb 04 2005 - 15:49:17 PST)
- AMBER: Is droplet boundary condition option possible ? Soo (Fri Feb 04 2005 - 22:18:36 PST)
- AMBER: loading pdb in leap to create parmeter files mrbroad.ilstu.edu (Sat Feb 05 2005 - 13:24:04 PST)
- AMBER: Tutorial Request Kara Di Giorgio (Sun Feb 06 2005 - 09:01:15 PST)
- AMBER: inconsistent ordering in an improper dihedral of TRP Sanghyun Park (Sun Feb 06 2005 - 20:38:03 PST)
- AMBER: correlation along PCA modes Vlad Cojocaru (Mon Feb 07 2005 - 03:35:44 PST)
- Re: AMBER: Creating an input file for GRASP using AMBER 8 Bill Ross (Mon Feb 07 2005 - 11:40:33 PST)
- AMBER: problem in writing Gustavo Pierdominici Sottile (Mon Feb 07 2005 - 11:59:49 PST)
- AMBER: How to calculate RESTRAINT value Mayumi Haga (Mon Feb 07 2005 - 20:09:25 PST)
- AMBER: dynamics error S.Sundar Raman (Tue Feb 08 2005 - 03:10:19 PST)
- AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel Fabien Cailliez (Tue Feb 08 2005 - 09:16:51 PST)
- AMBER: problem in minimization Gustavo Pierdominici Sottile (Tue Feb 08 2005 - 10:31:17 PST)
- AMBER: Minimization Beale, John (Tue Feb 08 2005 - 11:30:52 PST)
- AMBER: Linux Enterprise Beale, John (Tue Feb 08 2005 - 11:39:54 PST)
- AMBER: Amber8 installation test possible failures Joe Nolan (Tue Feb 08 2005 - 11:55:39 PST)
- AMBER: leap bond angle building Stern, Julie (Tue Feb 08 2005 - 15:44:39 PST)
- Re: AMBER: leap bond angle building Bill Ross (Tue Feb 08 2005 - 16:00:12 PST)
- AMBER: minimize a ptraj average pdb structure Eric Hu (Tue Feb 08 2005 - 17:48:26 PST)
- AMBER: energy plot in minimization Gustavo Pierdominici Sottile (Wed Feb 09 2005 - 09:36:25 PST)
- AMBER: stereo Filip Lankas (Wed Feb 09 2005 - 09:53:45 PST)
- AMBER: question about mm_gbsa output file michael chen (Wed Feb 09 2005 - 10:10:06 PST)
- AMBER: Convert to Pdb Beale, John (Wed Feb 09 2005 - 11:03:27 PST)
- AMBER: minimization.out Gustavo Pierdominici Sottile (Wed Feb 09 2005 - 11:32:01 PST)
- AMBER: DIVCON optimization Kara Di Giorgio (Wed Feb 09 2005 - 11:46:03 PST)
- AMBER: Can REM be used as multiple normal sander jobs on parallel machine qlu.notes.cc.sunysb.edu (Wed Feb 09 2005 - 15:15:59 PST)
- AMBER: desc NEWRES and blank unit type Stern, Julie (Wed Feb 09 2005 - 18:07:00 PST)
- AMBER: question about surface area to GBsurf calculation michael chen (Wed Feb 09 2005 - 22:20:58 PST)
- AMBER: Another question about surface area calculation michael chen (Wed Feb 09 2005 - 22:26:00 PST)
- AMBER: Poisson Boltzmann dynamics error Rachel Burdge (Thu Feb 10 2005 - 08:04:55 PST)
- AMBER: Protonate state of ARG and LYS. Liu, Jingyuan (Thu Feb 10 2005 - 13:56:39 PST)
- AMBER: How to converts a binary mdcrd file thanyarat Udom (Thu Feb 10 2005 - 23:02:21 PST)
- AMBER: How to converts a binary mdcrd file thanyarat Udom (Fri Feb 11 2005 - 00:00:10 PST)
- AMBER: Cu++ and RED Cenk Andac (Fri Feb 11 2005 - 01:46:13 PST)
- AMBER: too much vacuum in the box created by Leap Marie-Pierre Durrieu (Fri Feb 11 2005 - 04:53:35 PST)
- AMBER: ptraj error and min problems Gustavo Pierdominici Sottile (Fri Feb 11 2005 - 06:54:23 PST)
- AMBER: archive Gustavo Pierdominici Sottile (Fri Feb 11 2005 - 06:58:33 PST)
- AMBER: reverse TI charge perturbation Eric Hu (Fri Feb 11 2005 - 17:59:10 PST)
- AMBER: S.Sundar Raman (Mon Feb 14 2005 - 01:03:27 PST)
- AMBER:how to analyse trajectory files S.Sundar Raman (Mon Feb 14 2005 - 01:17:39 PST)
- AMBER: vlimit Gustavo Pierdominici Sottile (Mon Feb 14 2005 - 04:23:31 PST)
- AMBER: AMBER 8 : Water cap problem Guillaume Bollot (Mon Feb 14 2005 - 05:14:20 PST)
- AMBER: constrains Gustavo Pierdominici Sottile (Mon Feb 14 2005 - 06:53:18 PST)
- AMBER: Restart Problem opitz.che.udel.edu (Mon Feb 14 2005 - 11:12:54 PST)
- AMBER: Mainchain example needed Kara Wald (Mon Feb 14 2005 - 13:43:06 PST)
- AMBER: running shell scripts in tleap? Cenk Andac (Mon Feb 14 2005 - 14:23:44 PST)
- AMBER: Topology Format Amber 8 Stuart Murdock (Tue Feb 15 2005 - 04:00:56 PST)
- AMBER: problems with running sander in parallel on linux Piotr Cieplak (Tue Feb 15 2005 - 10:28:02 PST)
- AMBER: blows up Gustavo Pierdominici Sottile (Tue Feb 15 2005 - 11:11:43 PST)
- AMBER: check in leap Gustavo Pierdominici Sottile (Tue Feb 15 2005 - 11:34:21 PST)
- AMBER: Cyclic peptide arubin.unmc.edu (Tue Feb 15 2005 - 13:12:28 PST)
- AMBER: PDB conversion to gzmat using antechamber Scott Pendley (Tue Feb 15 2005 - 15:32:21 PST)
- AMBER: EWALD and belly not strictly correct Stern, Julie (Tue Feb 15 2005 - 21:41:49 PST)
- AMBER: Why I couldnt used carnal for analyzed RMSD ? thanyarat Udom (Wed Feb 16 2005 - 01:28:17 PST)
- AMBER: Gustavo Pierdominici Sottile (Wed Feb 16 2005 - 04:22:59 PST)
- AMBER: rms Gustavo Pierdominici Sottile (Wed Feb 16 2005 - 05:14:50 PST)
- AMBER: Beale, John (Wed Feb 16 2005 - 05:42:26 PST)
- AMBER: Phi-Psi-Energy plot L Jin (Wed Feb 16 2005 - 07:45:18 PST)
- AMBER: generate charmm paramater file from amber parm file HL Eastwood (Wed Feb 16 2005 - 09:19:56 PST)
- Re: AMBER: Why I couldnt used carnal for analyzed RMSD ? Bill Ross (Wed Feb 16 2005 - 10:19:30 PST)
- AMBER: Amber7 nmropt Markus W. Germann (Wed Feb 16 2005 - 13:09:08 PST)
- AMBER: installation of amber 8 on windows anshul.imtech.res.in (Thu Feb 17 2005 - 12:17:11 PST)
- AMBER: Re: pmemd problems Robert Duke (Thu Feb 17 2005 - 07:15:33 PST)
- AMBER: rotameric populations? Cenk Andac (Thu Feb 17 2005 - 07:15:05 PST)
- AMBER: moil-view Beale, John (Thu Feb 17 2005 - 07:56:30 PST)
- AMBER: Antechamber help needed Kara Di Giorgio (Thu Feb 17 2005 - 09:24:34 PST)
- AMBER: Moil view trajectory clusters Austin B. Yongye (Thu Feb 17 2005 - 09:36:15 PST)
- AMBER: problem with ptraj and randomizeions Fabien Cailliez (Thu Feb 17 2005 - 09:56:24 PST)
- AMBER: PSC Summer Workshop: Modeling Proteins and Nucleic Acids with AMBER, VMD and the MMTSB Toolkit Troy Wymore (Thu Feb 17 2005 - 11:00:36 PST)
- AMBER: amber8 and moil-view Lihua Wang (Thu Feb 17 2005 - 11:26:32 PST)
- AMBER: Amber8 Solaris installation failure Joe Nolan (Thu Feb 17 2005 - 12:27:12 PST)
- AMBER: sander errors with atom restraints on ia64 Rachel Burdge (Thu Feb 17 2005 - 13:46:04 PST)
- AMBER: leap saveamberparm chain types response Stern, Julie (Thu Feb 17 2005 - 15:16:50 PST)
- AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) Greg Recine (Thu Feb 17 2005 - 16:23:01 PST)
- Re: AMBER: leap saveamberparm chain types response Bill Ross (Thu Feb 17 2005 - 17:15:20 PST)
- AMBER: GB solvation and "boxed" environment simulation Soo (Thu Feb 17 2005 - 21:32:38 PST)
- AMBER: molecule blowing apart during equilibration Stern, Julie (Thu Feb 17 2005 - 23:12:16 PST)
- AMBER: ptraj Gustavo Pierdominici Sottile (Fri Feb 18 2005 - 06:58:37 PST)
- AMBER: XMGR Beale, John (Fri Feb 18 2005 - 10:20:44 PST)
- AMBER: DNA Tutorial Dwayne Hoobler (Fri Feb 18 2005 - 15:07:34 PST)
- AMBER: Amber: sander error segmentation fault. S.Sundar Raman (Fri Feb 18 2005 - 22:03:50 PST)
- AMBER: ptraj for RDF calculations Javier Perez Miron (Sat Feb 19 2005 - 08:47:02 PST)
- AMBER: simulation with explicit water molecules Ye MEI (Sat Feb 19 2005 - 19:24:48 PST)
- AMBER: (no subject) yen li (Sun Feb 20 2005 - 10:16:32 PST)
- AMBER: AIX problem Mayumi Haga (Sun Feb 20 2005 - 21:17:29 PST)
- AMBER: ptraj for RDF calculations Javier Perez Miron (Mon Feb 21 2005 - 00:42:33 PST)
- AMBER: Amber 8 with lam compilation problem m m (Mon Feb 21 2005 - 00:55:49 PST)
- AMBER: problem with protein minimization yen li (Mon Feb 21 2005 - 01:12:02 PST)
- AMBER: separate solvent-solvent and solvent-solute interaction Ye MEI (Mon Feb 21 2005 - 04:44:22 PST)
- AMBER: Formatting Questions Kara Di Giorgio (Mon Feb 21 2005 - 11:09:44 PST)
- AMBER: Free energy extimate for the same structure but different conformers claudio (Mon Feb 21 2005 - 12:56:10 PST)
- AMBER: ptraj problem Mayumi Haga (Tue Feb 22 2005 - 01:38:43 PST)
- AMBER: restraint only for Z cartegian coordinate? Jaroslav Hanus (Tue Feb 22 2005 - 07:40:58 PST)
- AMBER: Restraint of atoms during minimization L Jin (Tue Feb 22 2005 - 08:17:05 PST)
- AMBER: dihedral driver? Beale, John (Tue Feb 22 2005 - 08:26:26 PST)
- AMBER: vlimit exceeded and temperature blow up Stern, Julie (Tue Feb 22 2005 - 08:36:05 PST)
- AMBER: MPI for sander8 S. Frank Yan (Tue Feb 22 2005 - 09:04:56 PST)
- AMBER: ptraj8: trajectory windows Anselm Horn (Tue Feb 22 2005 - 09:16:13 PST)
- AMBER: lastrst Stern, Julie (Tue Feb 22 2005 - 15:06:24 PST)
- AMBER: lastrst Stern, Julie (Tue Feb 22 2005 - 17:21:00 PST)
- AMBER: minimizing structures before MM-PBSA? scopio (Tue Feb 22 2005 - 17:23:37 PST)
- AMBER: convert one functional group to another with TI Eric Hu (Tue Feb 22 2005 - 17:29:42 PST)
- AMBER: total energy of solvation Holly Freedman (Tue Feb 22 2005 - 20:05:36 PST)
- AMBER: size of solventbox mathew k varghese (Tue Feb 22 2005 - 20:07:00 PST)
- AMBER: mpirun sander8 problem S. Frank Yan (Tue Feb 22 2005 - 23:13:34 PST)
- AMBER: RE:Amber 8 with lam compilation problem Maciej KA (Wed Feb 23 2005 - 00:07:37 PST)
- Re: AMBER: lastrst Stern, Julie (Wed Feb 23 2005 - 13:03:57 PST)
- AMBER: classes Gustavo Pierdominici Sottile (Wed Feb 23 2005 - 13:00:47 PST)
- AMBER: solvateOct method Cameron Mura (Wed Feb 23 2005 - 18:26:19 PST)
- Re: AMBER: Use of ibelly with nmode analysis marti (Thu Feb 24 2005 - 03:47:28 PST)
- AMBER: How to build dynamics input for guanine with tleap ? Maciej (Thu Feb 24 2005 - 05:44:37 PST)
- AMBER: Joining residues/units Bogos Agianian (Thu Feb 24 2005 - 06:58:55 PST)
- AMBER: cross-correlation Xin Hu (Thu Feb 24 2005 - 08:40:54 PST)
- AMBER: ambpdb radii Harianto (Thu Feb 24 2005 - 11:24:39 PST)
- AMBER: units describing projection onto modes Vlad Cojocaru (Thu Feb 24 2005 - 10:40:18 PST)
- AMBER: correlation Gustavo Pierdominici Sottile (Thu Feb 24 2005 - 11:48:50 PST)
- AMBER: pmemd + pgi 5.1 + ntr = 1 Peter Varnai (Thu Feb 24 2005 - 14:25:04 PST)
- AMBER: My last posting Robert Duke (Thu Feb 24 2005 - 20:15:08 PST)
- AMBER: compile amber8 on RHEL4 HuiZhe Li (Thu Feb 24 2005 - 23:59:02 PST)
- AMBER: nmode entropy calculations in MMPBSA Fabien Cailliez (Fri Feb 25 2005 - 02:20:23 PST)
- AMBER: vlimit Gustavo Pierdominici Sottile (Fri Feb 25 2005 - 04:45:35 PST)
- AMBER: make test.lmod error yuann (Fri Feb 25 2005 - 08:45:11 PST)
- AMBER: setBox buffer in leap Stern, Julie (Fri Feb 25 2005 - 10:43:19 PST)
- AMBER: problem with solvateBox ReichertD.mir.wustl.edu (Fri Feb 25 2005 - 12:38:51 PST)
- AMBER: Austin B. Yongye (Fri Feb 25 2005 - 13:43:56 PST)
- AMBER: ico(i)=-1? Xiao He (Fri Feb 25 2005 - 19:49:46 PST)
- AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem praveena moldy (Sun Feb 27 2005 - 21:36:36 PST)
- AMBER: GBSA calculation Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Mon Feb 28 2005 - 02:59:23 PST)
- AMBER: creating a new residue Amber admin (Mon Feb 28 2005 - 08:44:59 PST)
- AMBER: Controlling number of water residues... Pavan G (Mon Feb 28 2005 - 23:14:51 PST)
- Last message date: Tue Mar 01 2005 - 07:53:00 PST
- Archived on: Fri Mar 12 2010 - 05:59:30 PST
