Amber Archive May 2006 by thread
- AMBER: Amber 9, sander imin = 5, -y flag z3020110.student.unsw.edu.au (Sun Apr 30 2006 - 18:08:44 PDT)
- Re: AMBER: error propagation in MM-PBSA binding free energy calculation Jianyin Shao (Mon May 01 2006 - 10:17:04 PDT)
- AMBER: sequential execution of number of parallel jobs In Hee Park (Mon May 01 2006 - 13:13:23 PDT)
- Re: AMBER: internal coordinates David A. Case (Mon May 01 2006 - 13:50:10 PDT)
- AMBER: distance restraints mkseo (Mon May 01 2006 - 14:49:21 PDT)
- AMBER: some new tutorials David A. Case (Mon May 01 2006 - 16:55:19 PDT)
- AMBER: How does amber calculate HB? Li Su (Mon May 01 2006 - 18:01:05 PDT)
- AMBER: AMBER Workshops, London UK 26th - 30th June 2006 Ross Walker (Tue May 02 2006 - 08:45:33 PDT)
- AMBER: Simulation of crystal - problem with excluded atom list Jennie Thomas (Tue May 02 2006 - 10:07:20 PDT)
- AMBER: MPI parallel problem in AMBER 8.0 mkseo (Tue May 02 2006 - 14:21:50 PDT)
- AMBER: Shared libraries error Andrew Box (Tue May 02 2006 - 20:14:38 PDT)
- AMBER: proper restart procedure? John J. Love (Tue May 02 2006 - 20:33:57 PDT)
- AMBER: Question bonds and angles in frcmod and lib files Jennie Thomas (Wed May 03 2006 - 01:02:55 PDT)
- AMBER: Error while running test.serial in Amber9 Priti Hansia (Wed May 03 2006 - 04:03:27 PDT)
- AMBER: cluster architecture for the best amber performance Kateryna Miroshnychenko (Wed May 03 2006 - 05:54:58 PDT)
- AMBER: concatenating .mdcrd files Kenley Barrett (Wed May 03 2006 - 09:31:59 PDT)
- AMBER: question about group format Holly Freedman (Wed May 03 2006 - 12:18:36 PDT)
- [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] Jennie Thomas (Wed May 03 2006 - 14:49:19 PDT)
- Re: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] Bill Ross (Wed May 03 2006 - 15:00:58 PDT)
- Re: AMBER: AMBER9: MacG5 parallel sander.MPI Mengjuei Hsieh (Wed May 03 2006 - 17:32:14 PDT)
- AMBER: Amber install on RedHat Linux a a (Wed May 03 2006 - 19:17:14 PDT)
- AMBER: carnal prob bala (Thu May 04 2006 - 00:44:53 PDT)
- AMBER: conflicting types for XawScrolledTableSetLocation K. Yarem (Thu May 04 2006 - 08:43:57 PDT)
- AMBER: molsurf.c error Miguel Ferreira (Thu May 04 2006 - 09:00:31 PDT)
- AMBER: amber9 serial compilation error Arvind Marathe (Thu May 04 2006 - 09:55:39 PDT)
- Re: AMBER: carnal prob Bill Ross (Thu May 04 2006 - 10:31:22 PDT)
- AMBER: lipid bi-layer system Lwin, ThuZar (Thu May 04 2006 - 10:41:11 PDT)
- AMBER: restraintmask Joseph Fernandez (Thu May 04 2006 - 11:22:21 PDT)
- AMBER: Problem with shared libraries: libimf.so Priti Hansia (Fri May 05 2006 - 10:55:39 PDT)
- AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson (Fri May 05 2006 - 11:37:19 PDT)
- AMBER: xleap on iMac G5 Evan Kelly (Fri May 05 2006 - 21:01:53 PDT)
- AMBER: AMBER9 INSTALLATION problem on O2 sgi system S.Sundar Raman (Sun May 07 2006 - 00:10:15 PDT)
- AMBER: xleap not recognizing residue Kenley Barrett (Sun May 07 2006 - 17:13:13 PDT)
- AMBER: question on distance calculation bala (Mon May 08 2006 - 03:09:23 PDT)
- AMBER: Amber9 test error on SGI Altix amit.mbu.iisc.ernet.in (Mon May 08 2006 - 10:14:19 PDT)
- AMBER: Problem with impose in lep Osmar Norberto de Souza (Mon May 08 2006 - 10:31:16 PDT)
- AMBER: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 Ross Walker (Mon May 08 2006 - 11:13:11 PDT)
- AMBER: Intel compiler version 9.0.033 Ross Walker (Mon May 08 2006 - 12:40:23 PDT)
- AMBER: PMEMD compilation error Joseph Fernandez (Mon May 08 2006 - 12:37:03 PDT)
- AMBER: About the Amber trajectories converted to XPLOR ( = DCD) format wang (Mon May 08 2006 - 23:25:47 PDT)
- AMBER: San Fransisco Amber users homeira amirkhani (Tue May 09 2006 - 04:38:06 PDT)
- AMBER: Amber9 test error on SGI Altix Priti Hansia (Tue May 09 2006 - 08:18:02 PDT)
- AMBER: RE: Intel Compiler. Ross Walker (Tue May 09 2006 - 09:05:28 PDT)
- AMBER: problem with prep file Simon Whitehead (Wed May 10 2006 - 03:52:32 PDT)
- AMBER: bug in ambpdb (AMBER8) Petr Kulhanek (Wed May 10 2006 - 03:54:55 PDT)
- AMBER: Hexahydrated Counterions Mahalakshmi Sahasranaman (Wed May 10 2006 - 06:22:02 PDT)
- [Fwd: AMBER: Problem with impose in lep] Osmar Norberto de Souza (Wed May 10 2006 - 10:09:48 PDT)
- Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why Kenley Barrett (Wed May 10 2006 - 12:54:46 PDT)
- AMBER: I'm very sorry, please disregard previous e-mail--problem seems to be fixed Kenley Barrett (Wed May 10 2006 - 13:04:16 PDT)
- AMBER: which patch for ioutfm = 1 in Amber8? Hannes Loeffler (Wed May 10 2006 - 22:21:25 PDT)
- AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1? Pan, Yongmei (Thu May 11 2006 - 07:13:02 PDT)
- AMBER: bond information in amber snoze pa (Thu May 11 2006 - 09:48:58 PDT)
- AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7 Pan, Yongmei (Thu May 11 2006 - 11:50:36 PDT)
- AMBER: Amber9/mpich2 performance Joseph Fernandez (Thu May 11 2006 - 15:30:03 PDT)
- AMBER: question about REDII Raffaella D'Auria (Thu May 11 2006 - 19:04:51 PDT)
- AMBER: AMBER 8 - dihedral angles when clambda=1 Ilyas Yildirim (Thu May 11 2006 - 21:57:37 PDT)
- AMBER: Xleap compilation problem Sergio Dall'Angelo (Fri May 12 2006 - 02:49:16 PDT)
- AMBER: Xleap compilation problem Sergio Dall'Angelo (Fri May 12 2006 - 03:19:48 PDT)
- AMBER: RMSD calculation between ligands Stefan Henrich (Fri May 12 2006 - 05:09:15 PDT)
- AMBER: another question: is rms 2E-2 good for nmode ntrun=1? Pan, Yongmei (Fri May 12 2006 - 08:22:00 PDT)
- AMBER: binpos file Varsha Goyal (Fri May 12 2006 - 13:46:24 PDT)
- AMBER: strange mm_pbsa output alfredoq.fcq.unc.edu.ar (Sat May 13 2006 - 08:44:58 PDT)
- AMBER: Compilers and libraries for AMBER in HPC! Pradipta Bandyopadhyay (Sun May 14 2006 - 06:25:07 PDT)
- AMBER: PBS script for lemieux Stern, Julie (Sun May 14 2006 - 16:09:30 PDT)
- AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs Zhihong Yu (Sun May 14 2006 - 20:55:51 PDT)
- AMBER: AMBER9 compilation error on IBM Cluster amit.mbu.iisc.ernet.in (Mon May 15 2006 - 04:11:50 PDT)
- AMBER: Problem with "impose" in leap Osmar Norberto de Souza (Mon May 15 2006 - 04:27:13 PDT)
- AMBER: fail to execute addles pang zhao (Mon May 15 2006 - 04:59:10 PDT)
- AMBER: ff02 + POL3 problem ! Pradipta Bandyopadhyay (Mon May 15 2006 - 06:53:20 PDT)
- AMBER: installation problem Mahalakshmi Sahasranaman (Mon May 15 2006 - 11:12:51 PDT)
- AMBER: density mathew k varghese (Mon May 15 2006 - 21:02:51 PDT)
- AMBER: amber8 compiled erro on opteron with 64 bit renyanliang (Tue May 16 2006 - 02:15:24 PDT)
- AMBER: trouble stripping waters with ptraj Adam Pelzer (Tue May 16 2006 - 13:09:30 PDT)
- AMBER: amber compilation on Red Hat 8 with MPICH kawamura_hiro.riken.jp (Tue May 16 2006 - 22:38:35 PDT)
- AMBER: "atom number exceeds the MAXATOM" BAUVAIS.itodys.jussieu.fr (Tue May 16 2006 - 22:54:24 PDT)
- AMBER: distance dependent dielectric constant Mahalakshmi Sahasranaman (Wed May 17 2006 - 03:36:55 PDT)
- AMBER: "The system has extended beyond" error message Atsutoshi Okabe (Wed May 17 2006 - 22:04:31 PDT)
- AMBER: Correlation matrix used in quasih (Amber 7) Craig Gough (Thu May 18 2006 - 00:06:03 PDT)
- AMBER: AMBER9 installation error on Compaq machine. Soonmin Jang (Thu May 18 2006 - 00:11:46 PDT)
- AMBER: vlimit exceeded aixiaoli (Thu May 18 2006 - 01:14:29 PDT)
- AMBER: problem with installation, or bug? Kenley Barrett (Thu May 18 2006 - 03:09:10 PDT)
- AMBER: force field parameters Douali, Latifa (Thu May 18 2006 - 10:33:35 PDT)
- AMBER: RMSd calculations Claire Zerafa (Thu May 18 2006 - 12:25:57 PDT)
- AMBER: OT: software to support AMBER? Steve Gwaltney (Thu May 18 2006 - 11:37:06 PDT)
- AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Hall, Spencer (Thu May 18 2006 - 15:44:14 PDT)
- AMBER: Intel fortran compiler 7? Simon Whitehead (Fri May 19 2006 - 02:47:55 PDT)
- AMBER: Fw: RMSd calculations Claire Zerafa (Fri May 19 2006 - 05:07:30 PDT)
- AMBER: problem loading forcefield leaprc.ff86 Mahalakshmi Sahasranaman (Fri May 19 2006 - 07:27:38 PDT)
- AMBER: RE: PMEMD compilation problems Simon Whitehead (Fri May 19 2006 - 08:37:46 PDT)
- AMBER: amber .off file format question Ilyas Yildirim (Fri May 19 2006 - 19:30:55 PDT)
- AMBER: RE: trouble stripping waters with ptraj Adam Pelzer (Sat May 20 2006 - 09:00:12 PDT)
- AMBER: Problem with running xleap remotely heaton.chem.utah.edu (Sat May 20 2006 - 12:20:27 PDT)
- AMBER: RMSd error Claire Zerafa (Mon May 22 2006 - 01:52:34 PDT)
- AMBER: Water density output Navnit Kumar Mishra (Mon May 22 2006 - 04:02:48 PDT)
- AMBER: A dummy atom on the center of solute molecule Atsutoshi Okabe (Mon May 22 2006 - 04:49:23 PDT)
- AMBER: Macromodel Amber* vs. Amber7 opitz.che.udel.edu (Mon May 22 2006 - 05:56:54 PDT)
- AMBER: More Amber 9 Benchmarks available Robert Duke (Mon May 22 2006 - 07:23:15 PDT)
- Re: AMBER: Problems compiling amber9 Don Harden (Mon May 22 2006 - 10:10:15 PDT)
- AMBER: Again SASA lucas luquitas (Mon May 22 2006 - 12:51:22 PDT)
- AMBER: 3Dsig: Struct Bioinfo & Comp Biophysics Meeting, 4-5 Aug. Brazil 3Dsig06 (Mon May 22 2006 - 15:03:45 PDT)
- AMBER: error in AMBER 9.0 mkseo (Tue May 23 2006 - 14:43:28 PDT)
- AMBER: amber8 bugfix effects kawamura_hiro.riken.jp (Wed May 24 2006 - 01:17:32 PDT)
- AMBER: simulate proteins with non-standard residues Hui Lei (Wed May 24 2006 - 10:10:08 PDT)
- AMBER: freeze interval vibrations Eric Hu (Wed May 24 2006 - 10:52:47 PDT)
- AMBER: problem with prepfile Shafinaz (Wed May 24 2006 - 12:50:21 PDT)
- AMBER: use_pme=0 problem luckyang.gmail.com (Wed May 24 2006 - 16:18:47 PDT)
- AMBER: output of first stage RESP calculation JunJun Liu (Wed May 24 2006 - 15:23:55 PDT)
- AMBER: How to built the deprotonated form of lysine and tyrosine jitrayut jitonnom (Wed May 24 2006 - 19:49:04 PDT)
- AMBER: Fwd: RESP for deprotonated tyrosine and lysine jitrayut jitonnom (Wed May 24 2006 - 19:57:45 PDT)
- AMBER: Qestion about input for RESP program JunJun Liu (Wed May 24 2006 - 19:44:41 PDT)
- AMBER: How to build NH2 of amino acid in amber jitrayut jitonnom (Wed May 24 2006 - 20:52:25 PDT)
- AMBER: question about QM/MM in amber9 aixiaoli (Thu May 25 2006 - 01:37:10 PDT)
- AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) Soonmin Jang (Thu May 25 2006 - 03:51:02 PDT)
- AMBER: 1st 2 lines of restart files hayden (Thu May 25 2006 - 04:40:03 PDT)
- AMBER: alpha helix preference problem harianto (Thu May 25 2006 - 14:16:23 PDT)
- AMBER: RMSd error Claire Zerafa (Thu May 25 2006 - 21:37:54 PDT)
- AMBER: RE: trouble stripping waters with ptraj Adam Pelzer (Thu May 25 2006 - 21:50:53 PDT)
- AMBER: ptraj: calculating distances between atoms in charges residues Magne Olufsen (Fri May 26 2006 - 00:13:48 PDT)
- AMBER: Question about .off file Sergey Krishtal (Fri May 26 2006 - 01:15:06 PDT)
- AMBER: different TI calculations starting from the same state Andrea Bortolato (Fri May 26 2006 - 06:56:47 PDT)
- AMBER: different TI calculations starting from the same state Andrea Bortolato (Fri May 26 2006 - 03:12:12 PDT)
- AMBER: Saving RMSD values in VMD nag raj (Fri May 26 2006 - 07:33:00 PDT)
- AMBER: check as error: load prepin in tleap jitrayut jitonnom (Fri May 26 2006 - 10:13:41 PDT)
- AMBER: Please reply Shafinaz (Fri May 26 2006 - 12:19:42 PDT)
- AMBER: Installing / Compiling Question Seth Lilavivat (Fri May 26 2006 - 20:29:06 PDT)
- AMBER: md error : sander jitrayut jitonnom (Sun May 28 2006 - 11:11:45 PDT)
- AMBER: which time should I use to calculate the number of "ps/Day" Zhihong Yu (Mon May 29 2006 - 02:32:26 PDT)
- AMBER: antechamber help needed for FAD pkb bioinfo (Mon May 29 2006 - 02:38:48 PDT)
- AMBER: Difference in results for TI calculation brmeher.iitg.ernet.in (Mon May 29 2006 - 06:53:41 PDT)
- AMBER: Difference in results for TI calculation brmeher.iitg.ernet.in (Mon May 29 2006 - 07:23:45 PDT)
- AMBER: problems with antechamber JAVIER PEREZ (Mon May 29 2006 - 08:04:52 PDT)
- AMBER: energy terms JAVIER PEREZ (Mon May 29 2006 - 08:25:31 PDT)
- AMBER: SAVEPDB in Xleap could not save 4 character atom names Jiayun Pang (Mon May 29 2006 - 09:38:22 PDT)
- Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names Bill Ross (Mon May 29 2006 - 13:26:56 PDT)
- AMBER: Different results for TI calculation Biswa Ranjan Meher (Wed May 31 2006 - 00:25:13 PDT)
- AMBER: Replica exchage: about exchange interval Atsutoshi Okabe (Wed May 31 2006 - 05:36:27 PDT)
- AMBER: Force units in forcedump.dat Steven Winfield (Wed May 31 2006 - 06:41:43 PDT)
- AMBER: Namelists in input files Steven Winfield (Wed May 31 2006 - 09:42:05 PDT)
- AMBER: SHAKE, TIP3P and 2fs Timesteps Mark Williamson (Wed May 31 2006 - 10:32:56 PDT)
- AMBER: xleap problem and answer Thomas Pochapsky (Wed May 31 2006 - 11:32:32 PDT)
- AMBER: AMBER mdcrd file bigger than 2GB snoze pa (Wed May 31 2006 - 14:57:22 PDT)
- AMBER: Installation of Amber8 on Fedora Core 5 DAVID P. RANGEL (Wed May 31 2006 - 15:48:11 PDT)
- Last message date: Sun Jun 04 2006 - 06:07:09 PDT
- Archived on: Mon Dec 23 2024 - 05:53:26 PST
