Amber Archive Apr 2007 by thread
- AMBER: phosphorylated residues yxamber (Sun Apr 01 2007 - 22:13:17 PDT)
- AMBER: Error at Equilibration.... Sandeep Kaushik (Mon Apr 02 2007 - 00:14:17 PDT)
- AMBER: Problem with sander.MPI Sandeep Kaushik (Mon Apr 02 2007 - 06:06:21 PDT)
- AMBER: RE: dihedral term charge dependence Williamson, Mark (Mon Apr 02 2007 - 09:07:29 PDT)
- AMBER: restraint command not taken deepti nayar (Mon Apr 02 2007 - 02:25:12 PDT)
- AMBER: Xleap errors Beale, John (Mon Apr 02 2007 - 10:20:43 PDT)
- AMBER: Cut off for cavities Sangwai, Ashishvikas (Mon Apr 02 2007 - 11:47:30 PDT)
- AMBER: Extra Points... How to Deal with Them David Cerutti (Mon Apr 02 2007 - 23:39:23 PDT)
- Re: AMBER: Problem with PCSHIFT module Edoardo Saccenti (Tue Apr 03 2007 - 01:08:38 PDT)
- AMBER: Sander.... Rita Cassia (Tue Apr 03 2007 - 01:23:06 PDT)
- AMBER: nmode Marie Brut (Tue Apr 03 2007 - 03:17:39 PDT)
- AMBER: Regarding Simulated Annealing Anju Sharma (Tue Apr 03 2007 - 05:27:18 PDT)
- AMBER: RE: dihedral term charge dependence Kateryna Miroshnychenko (Tue Apr 03 2007 - 06:59:08 PDT)
- AMBER: sander bomb janavi raghavan (Tue Apr 03 2007 - 07:28:39 PDT)
- RE: AMBER: enzyme kinetics in silico Xu, Yong (Tue Apr 03 2007 - 12:26:45 PDT)
- Re: AMBER: enzyme kinetics in silico Sean Rathlef (Tue Apr 03 2007 - 14:08:10 PDT)
- AMBER: principal axis calculation in Ptraj Esther Brugger (Tue Apr 03 2007 - 14:05:44 PDT)
- AMBER: Energy minimization problem Bo Baker (Tue Apr 03 2007 - 18:24:05 PDT)
- AMBER: about define improper torsion in .frcmod file Chengwen Chen (Wed Apr 04 2007 - 02:02:57 PDT)
- AMBER: parse radii AYTUG TUNCEL (Wed Apr 04 2007 - 02:10:10 PDT)
- AMBER: FW: parameter Ross Walker (Wed Apr 04 2007 - 08:18:07 PDT)
- AMBER: choice of alpha carbons vs side chains Christopher Gaughan (Wed Apr 04 2007 - 15:34:31 PDT)
- Re: AMBER: choice of alpha carbons vs side chains Bill Ross (Wed Apr 04 2007 - 16:28:34 PDT)
- AMBER: Charges in antechamber Beale, John (Thu Apr 05 2007 - 08:46:34 PDT)
- AMBER: Problems during compilation and test. Liang, Lei (Thu Apr 05 2007 - 13:43:23 PDT)
- AMBER: principal mask dorotation Esther Brugger (Thu Apr 05 2007 - 14:46:51 PDT)
- AMBER: amber 9 installation: broken pipe Stern, Julie (Thu Apr 05 2007 - 16:54:16 PDT)
- AMBER: MD at constan pH tri nam Vo (Fri Apr 06 2007 - 07:10:18 PDT)
- AMBER: Blue Gene, compile Amber9? Mike Hanby (Fri Apr 06 2007 - 10:22:57 PDT)
- AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag) Chris Moth (Fri Apr 06 2007 - 11:50:29 PDT)
- AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report) Chris Moth (Fri Apr 06 2007 - 14:07:17 PDT)
- AMBER: PDB file format for AMBER Neelanjana Sengupta (Fri Apr 06 2007 - 19:41:43 PDT)
- Re: AMBER: pH effect on protein folding tri nam Vo (Fri Apr 06 2007 - 23:27:40 PDT)
- AMBER: Extra points... virial computation David Cerutti (Sat Apr 07 2007 - 23:48:11 PDT)
- AMBER: ptraj:problems with time correlation calculation (comp. with NMR experiments) anna.schrey.gmx.de (Sun Apr 08 2007 - 05:21:38 PDT)
- AMBER: supplement ptraj:problems with time correlation calculation (comp. with NMR experiments) anna.schrey.gmx.de (Sun Apr 08 2007 - 07:15:22 PDT)
- AMBER: ptraj hbond Evan Kelly (Sun Apr 08 2007 - 17:37:04 PDT)
- AMBER: Fails to load libraries present in /leap/lib/ Neelanjana Sengupta (Mon Apr 09 2007 - 02:33:29 PDT)
- AMBER: Vlad has Tagged you! :) Vlad Cojocaru (Mon Apr 09 2007 - 03:06:37 PDT)
- AMBER: NTX=7 ?............lastist= ?...........lastrst= ????? Sandeep Kaushik (Mon Apr 09 2007 - 03:35:54 PDT)
- AMBER: I'm sorry ... please ignore the junk !! Vlad Cojocaru (Mon Apr 09 2007 - 03:50:54 PDT)
- AMBER: Question about MMPBSA v9 Cenk Andac (Mon Apr 09 2007 - 03:54:39 PDT)
- AMBER: Constant volume simulations Christopher Gaughan (Mon Apr 09 2007 - 11:59:26 PDT)
- AMBER: Sander Bomb in subroutine nonbond_list Jingyuan Luke (Mon Apr 09 2007 - 19:34:51 PDT)
- AMBER: Problem while using antechamber Anju Sharma (Mon Apr 09 2007 - 23:15:47 PDT)
- AMBER: problem related to visualizing of structure deepti nayar (Mon Apr 09 2007 - 23:33:40 PDT)
- AMBER: sander (AMBER 9) and -y flag -- not working? David Mobley (Tue Apr 10 2007 - 11:22:39 PDT)
- Re: AMBER: how to modify map.DG-AMBER file? A Box (Tue Apr 10 2007 - 16:56:21 PDT)
- AMBER: amber9: running parallel error Khatcharin Siriwong (Wed Apr 11 2007 - 01:08:16 PDT)
- AMBER: Prblm rgrdng Simulated Annealing Anju Sharma (Wed Apr 11 2007 - 03:06:08 PDT)
- AMBER: Problem with Sander restart file. Martin Stennett (Wed Apr 11 2007 - 03:56:37 PDT)
- AMBER: temperature artifacts with andersen and GB? David Mobley (Wed Apr 11 2007 - 09:50:17 PDT)
- AMBER: working with Antechamber Atila Iamarino (Wed Apr 11 2007 - 10:45:20 PDT)
- AMBER: CHARMM vs. AMBER ff literature Seth Lilavivat (Wed Apr 11 2007 - 08:21:07 PDT)
- AMBER: Attaching capping groups Neelanjana Sengupta (Wed Apr 11 2007 - 18:28:33 PDT)
- AMBER: Needed help regardng Simulated Annealing Anju Sharma (Wed Apr 11 2007 - 22:07:14 PDT)
- AMBER: How can I modify the frcmod file of ligand with a nonstandard guanidine tonglei (Thu Apr 12 2007 - 00:13:34 PDT)
- AMBER: topology for postprocessed files? anna.schrey.gmx.de (Thu Apr 12 2007 - 02:57:28 PDT)
- AMBER: bad atom type errors in GB for halides? David Mobley (Thu Apr 12 2007 - 10:19:51 PDT)
- AMBER: Multiple Bonds to one Atom crowfoot.unr.nevada.edu (Thu Apr 12 2007 - 13:41:36 PDT)
- AMBER: polarization and water density Thérèse Malliavin (Fri Apr 13 2007 - 02:36:44 PDT)
- AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275 Arvind Marathe (Fri Apr 13 2007 - 03:23:38 PDT)
- AMBER: Amber:PBSA&Extract_coords problem (Needed help) odde (Fri Apr 13 2007 - 12:06:42 PDT)
- AMBER: QMMM with printcharges Kijeong Kwac (Fri Apr 13 2007 - 17:37:45 PDT)
- AMBER: mdfil.f Peljidiyn Genden (Sat Apr 14 2007 - 00:43:27 PDT)
- AMBER: Amber 8 support of CHARMM ff? Seth Lilavivat (Sat Apr 14 2007 - 11:36:35 PDT)
- AMBER: Release of the R.E.D.-III tools FyD (Sun Apr 15 2007 - 03:10:25 PDT)
- AMBER: membrane simulation Jojart Balazs (Sun Apr 15 2007 - 11:06:31 PDT)
- AMBER: H-bond analysis............acceptorH absent..!!! Sandeep Kaushik (Sun Apr 15 2007 - 23:32:28 PDT)
- AMBER: Projecting trajectories onto normal modes Harald Lanig (Mon Apr 16 2007 - 07:50:38 PDT)
- AMBER: ptraj and quasi harmonic analysis Hans Lee (Mon Apr 16 2007 - 14:19:34 PDT)
- AMBER: MM-PBSA_binding energy script error odde (Mon Apr 16 2007 - 16:33:14 PDT)
- AMBER: Re: amber mm-pbsa problem Jiten (Mon Apr 16 2007 - 18:39:26 PDT)
- AMBER: problem with calculating RMSD tri nam Vo (Tue Apr 17 2007 - 00:01:35 PDT)
- AMBER: vmd and amber deepti nayar (Tue Apr 17 2007 - 04:58:51 PDT)
- AMBER: PDBs Beale, John (Tue Apr 17 2007 - 05:22:42 PDT)
- AMBER: ptraj secstruct core dumped error vijayaraj.clri.info (Tue Apr 17 2007 - 06:45:04 PDT)
- AMBER: Request for addition of a useful command in ptraj module of AMBER Cenk Andac (Tue Apr 17 2007 - 10:18:30 PDT)
- AMBER: Request for addition of a useful command in ptraj module of AMBER #2 Cenk Andac (Tue Apr 17 2007 - 10:24:37 PDT)
- AMBER: Re: MM-PBSA amber script problem odde (Tue Apr 17 2007 - 11:45:06 PDT)
- AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? Nicolas Lux Fawzi (Tue Apr 17 2007 - 12:00:18 PDT)
- AMBER: using glycam04 parameters Sara Alexandra Moura (Tue Apr 17 2007 - 12:17:44 PDT)
- AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? 2nd try Nicolas Lux Fawzi (Tue Apr 17 2007 - 14:50:07 PDT)
- AMBER: frcmod file deepti nayar (Tue Apr 17 2007 - 23:31:52 PDT)
- AMBER: printcharges option when using QM/MM simulation 한재범 (Tue Apr 17 2007 - 23:41:33 PDT)
- AMBER: Protonation/deprotonation of terminal residues Jesper Soerensen (Wed Apr 18 2007 - 05:56:26 PDT)
- AMBER: signal SIGSEGV(11) Pankaj R. Daga (Wed Apr 18 2007 - 08:25:55 PDT)
- AMBER: ff02 + POL3 - polar interactions !! Pradipta Bandyopadhyay (Wed Apr 18 2007 - 09:04:22 PDT)
- AMBER: Antechamber Warning Beale, John (Wed Apr 18 2007 - 12:39:31 PDT)
- AMBER: ptraj bug? Tamara Rogers (Wed Apr 18 2007 - 15:09:39 PDT)
- AMBER: Sander BOMB.. simulation terminates by itself... Vijay Manickam Achari (Wed Apr 18 2007 - 18:24:28 PDT)
- AMBER: Ewald BOMB....... what is this.. Vijay Manickam Achari (Wed Apr 18 2007 - 20:13:38 PDT)
- AMBER: Antechamber Beale, John (Thu Apr 19 2007 - 06:51:03 PDT)
- AMBER: regarding frcmod file Santanu Roy (Thu Apr 19 2007 - 08:28:01 PDT)
- AMBER: RE: RE: AMBER: QMMM with printcharges Kijeong Kwac (Thu Apr 19 2007 - 08:42:38 PDT)
- AMBER: Problems with Machine file for sander.MPI Terry Lang (Thu Apr 19 2007 - 13:15:45 PDT)
- AMBER: AIX 5 test failures: -NaNQ Patrick McCarren (Thu Apr 19 2007 - 16:30:35 PDT)
- AMBER: QM/MM NPT Simulation Daniel Oehme (Thu Apr 19 2007 - 21:46:14 PDT)
- AMBER: A test email Ruchi Sachdeva (Thu Apr 19 2007 - 23:54:55 PDT)
- AMBER: process and plot matrix data Vlad Cojocaru (Fri Apr 20 2007 - 02:28:12 PDT)
- AMBER: rigid epoxide substrate Dr M. Blomberg (Fri Apr 20 2007 - 04:24:13 PDT)
- AMBER: restraint value: written but none specified Ben Sattelle (Fri Apr 20 2007 - 13:42:56 PDT)
- AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out" Khatcharin Siriwong (Sat Apr 21 2007 - 00:42:14 PDT)
- AMBER: mol2 format Jardas sucuriba (Sun Apr 22 2007 - 15:57:12 PDT)
- AMBER: .prmtop entries Neelanjana Sengupta (Sun Apr 22 2007 - 22:53:46 PDT)
- AMBER: problem regarding implicit simulation gurpreet singh (Sun Apr 22 2007 - 23:16:35 PDT)
- AMBER: MM-PBSA: decompose energy error jitrayut jitonnom (Mon Apr 23 2007 - 04:31:43 PDT)
- Re: AMBER: is possible to compile pmemd using scali MPI? Andrea Bortolato (Mon Apr 23 2007 - 05:31:53 PDT)
- AMBER: MM-PBSA: Can't finish the binding energy process jitrayut jitonnom (Mon Apr 23 2007 - 05:34:48 PDT)
- AMBER: Problem using Ptraj alfredoq.fcq.unc.edu.ar (Mon Apr 23 2007 - 08:41:56 PDT)
- AMBER: Problems with AMBER8 on 32-bit FC6 David LeBard (Mon Apr 23 2007 - 11:51:02 PDT)
- AMBER: Error on compile amber8 tri nam Vo (Mon Apr 23 2007 - 22:04:34 PDT)
- AMBER: QM/MM simulation with SCC-DFTB 한재범 (Tue Apr 24 2007 - 01:19:25 PDT)
- AMBER: amber equation of ff99 Chengwen Chen (Tue Apr 24 2007 - 09:13:54 PDT)
- Re: AMBER:a question about RMSD Carlos Simmerling (Tue Apr 24 2007 - 06:06:40 PDT)
- AMBER: NAD parameters Jardas sucuriba (Tue Apr 24 2007 - 11:02:56 PDT)
- AMBER: mobile proton algorithm HL Eastwood (Tue Apr 24 2007 - 12:25:10 PDT)
- AMBER: Error on compiling AMBER8 tri nam Vo (Tue Apr 24 2007 - 19:03:16 PDT)
- AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38 Ruchi Sachdeva (Tue Apr 24 2007 - 20:54:14 PDT)
- AMBER: Work with constand pH tri nam Vo (Wed Apr 25 2007 - 01:13:05 PDT)
- AMBER: Employing SCC-DFTB with a periodic boundary condtion 한재범 (Wed Apr 25 2007 - 23:48:58 PDT)
- AMBER: protein-rna interaction & mmpbsa Antonio Morreale (Thu Apr 26 2007 - 01:28:19 PDT)
- AMBER: Problems installing Amber9 Ângela dos Reis (Fri Apr 27 2007 - 04:14:05 PDT)
- AMBER: Error in protonating Neelanjana Sengupta (Fri Apr 27 2007 - 04:31:52 PDT)
- AMBER: Print individual free energies in MD trajectories using MM_PBSA Giulio Rastelli (Fri Apr 27 2007 - 09:05:39 PDT)
- AMBER: QM/MM Umbrella sampling Jason DeChancie (Fri Apr 27 2007 - 13:53:08 PDT)
- AMBER: thermodynamic integration Servaas Michielssens (Sat Apr 28 2007 - 10:48:10 PDT)
- AMBER: Binding free energy errors: Grid setting fail jitrayut jitonnom (Sun Apr 29 2007 - 06:48:17 PDT)
- AMBER: a problem of surface area calulated by MM/PBSA Chengwen Chen (Mon Apr 30 2007 - 00:34:38 PDT)
- AMBER: Problem with MM-PBSA statistics Henar Martínez García (Mon Apr 30 2007 - 02:53:38 PDT)
- AMBER: Problem with calcpka.pl and constant pH Hayden Eastwood (Mon Apr 30 2007 - 04:35:23 PDT)
- AMBER: Problem with calcpka.pl and constant pH Hayden Eastwood (Mon Apr 30 2007 - 06:04:11 PDT)
- AMBER: PDB files Beale, John (Mon Apr 30 2007 - 09:16:59 PDT)
- AMBER: pressure tensor in a slab configuration rdauria.uci.edu (Mon Apr 30 2007 - 19:16:08 PDT)
- Last message date: Wed May 02 2007 - 06:07:23 PDT
- Archived on: Mon Dec 23 2024 - 05:53:31 PST
