Amber Archive Jul 2006 By Thread
- Re: AMBER: How to calculate binding free energy using MM-PBSA Xioling Chuang (Fri Jun 30 2006 - 21:39:09 PDT)
- AMBER: pmemd9 issue Brent Krueger (Sat Jul 01 2006 - 20:45:11 PDT)
- AMBER: R.E.D II Franck_Vendeix.ncsu.edu (Sun Jul 02 2006 - 19:11:39 PDT)
- AMBER: compiling amber9 nadiav.soton.ac.uk (Mon Jul 03 2006 - 01:50:44 PDT)
- Re: AMBER: NAMOT Andreas Svrcek-Seiler (Mon Jul 03 2006 - 04:02:57 PDT)
- AMBER: fixing residues Prabhakar. G. (Mon Jul 03 2006 - 05:16:46 PDT)
- AMBER: 2-D free energy surface using WHAM Atsutoshi Okabe (Mon Jul 03 2006 - 05:08:01 PDT)
- AMBER: multiple "restraint_wt" in sander kanazta1.yahoo.co.jp (Mon Jul 03 2006 - 07:12:21 PDT)
- AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux frustrated modeller (Mon Jul 03 2006 - 10:51:13 PDT)
- RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. . Lwin, ThuZar (Mon Jul 03 2006 - 12:02:31 PDT)
- AMBER: hbond analysis Claire Zerafa (Mon Jul 03 2006 - 14:06:22 PDT)
- AMBER: Dihedral analysis Claire Zerafa (Mon Jul 03 2006 - 14:25:33 PDT)
- AMBER: MM-PBSA: Problem when Generating Snapshots Zu Thur Yew (Tue Jul 04 2006 - 00:20:39 PDT)
- AMBER: Constant pH simulation : LYS residue Guillaume Bollot (Tue Jul 04 2006 - 04:13:00 PDT)
- AMBER: hbond analysis2 Claire Zerafa (Tue Jul 04 2006 - 07:00:35 PDT)
- AMBER: Can you use VMD to measure bond angles/lengths sethl.gatech.edu (Tue Jul 04 2006 - 08:24:49 PDT)
- Re: AMBER: problems about compiling a parallel version of AMBER 9 Chengwen Chen (Tue Jul 04 2006 - 21:29:38 PDT)
- AMBER: error on running parallel sander on remote node- amber9 Chengwen Chen (Wed Jul 05 2006 - 00:46:11 PDT)
- AMBER: problem with saving the parameters file amere swathi (Wed Jul 05 2006 - 01:50:40 PDT)
- AMBER: analysis of atoms in a range during simulation pkb bioinfo (Wed Jul 05 2006 - 05:41:58 PDT)
- Re: AMBER: manual/prmtop/missing bonds section David A. Case (Wed Jul 05 2006 - 09:09:06 PDT)
- AMBER: Question about Energy calculation using MM-PBSA scripts & Imaging Zu Thur Yew (Wed Jul 05 2006 - 10:03:13 PDT)
- AMBER: Namot on AMD 64 possible sethl.gatech.edu (Wed Jul 05 2006 - 10:05:26 PDT)
- AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) Ray Luo (Wed Jul 05 2006 - 10:45:49 PDT)
- Re: AMBER: problem with saving the parameters file Bill Ross (Wed Jul 05 2006 - 11:23:05 PDT)
- AMBER: igb=2 and "bad atom type" conflict Evan Kelly (Wed Jul 05 2006 - 12:25:16 PDT)
- AMBER: Addendum: igb=2 and "bad atom type" conflict Evan Kelly (Wed Jul 05 2006 - 12:29:10 PDT)
- AMBER: change atom in a DNA double strand Carra, Claudio \(JSC-SK\)[USRA] (Wed Jul 05 2006 - 14:09:23 PDT)
- Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. David A. Case (Wed Jul 05 2006 - 14:31:14 PDT)
- AMBER: PTRAJ OUTPUT Cporteli (Wed Jul 05 2006 - 16:02:47 PDT)
- RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .. . Lwin, ThuZar (Wed Jul 05 2006 - 16:01:25 PDT)
- Re: AMBER: PTRAJ OUTPUT Bill Ross (Wed Jul 05 2006 - 16:43:57 PDT)
- AMBER: Units for Leonard-Jones potential parameters Vanessa Oklejas (Wed Jul 05 2006 - 20:02:59 PDT)
- AMBER: analysis of ATOMs in ´certain range distance during simulation pkb bioinfo (Wed Jul 05 2006 - 20:37:46 PDT)
- AMBER: Compiling AMBER 9 on windows XP using cygwin Gobind Bisht (Wed Jul 05 2006 - 22:17:54 PDT)
- AMBER: Re: Strange problems with PMEMD on Intel Xeons with Infiniband Fabian Boes (Thu Jul 06 2006 - 01:29:35 PDT)
- AMBER: working with large strained system Tanya Johannsen (Wed Jul 05 2006 - 19:29:58 PDT)
- AMBER: Problem with bcc flag of antechamber Gobind Bisht (Thu Jul 06 2006 - 10:00:49 PDT)
- Re: AMBER: working with large strained system Bill Ross (Thu Jul 06 2006 - 10:06:57 PDT)
- AMBER: Problem with bcc flag of antechamber..continued Gobind Bisht (Thu Jul 06 2006 - 10:08:45 PDT)
- AMBER: Problem with donor/acceptor specification in ptraj hbonding facilities Thomas Steinbrecher (Thu Jul 06 2006 - 16:02:19 PDT)
- AMBER: Sander NOE violations Andrew Box (Thu Jul 06 2006 - 16:55:59 PDT)
- AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ? Christophe Guilbert (Thu Jul 06 2006 - 17:51:49 PDT)
- AMBER: Amber8.0 predictied pKa problem for a Lysine! Guillaume Bollot (Fri Jul 07 2006 - 02:38:08 PDT)
- AMBER: calculating dihedral angles, radius of gyration madhumalar.bii-sg.org (Fri Jul 07 2006 - 02:57:14 PDT)
- AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag Bob Johnson (Fri Jul 07 2006 - 07:55:32 PDT)
- AMBER: script to extract data from minimization .out file Tanya Johannsen (Fri Jul 07 2006 - 09:55:44 PDT)
- AMBER: Error in loading molecule in tleap Gobind Bisht (Fri Jul 07 2006 - 11:01:45 PDT)
- AMBER: AMBER 8: Problem with MPI_Finalize jrd (Fri Jul 07 2006 - 11:24:08 PDT)
- AMBER: convert chemical structure to pdb file Baker, Bo-Yang (Fri Jul 07 2006 - 11:44:25 PDT)
- AMBER: MM/PBSA Wei Chen (Fri Jul 07 2006 - 14:20:47 PDT)
- AMBER: Error in running MD in sander Gobind Bisht (Sat Jul 08 2006 - 10:20:10 PDT)
- AMBER: peptide simulation before docking jitrayut jitonnom (Sat Jul 08 2006 - 13:45:28 PDT)
- AMBER: Fwd: ADL: peptide simulation before docking jitrayut jitonnom (Sun Jul 09 2006 - 02:26:59 PDT)
- AMBER: (no subject) Andrew Box (Sun Jul 09 2006 - 15:49:02 PDT)
- AMBER: Replica exchange Atsutoshi Okabe (Mon Jul 10 2006 - 04:38:17 PDT)
- AMBER: residue and atom number Andrea Bortolato (Mon Jul 10 2006 - 05:57:05 PDT)
- AMBER: about restraint format. Qingning Shu (Mon Jul 10 2006 - 06:11:16 PDT)
- AMBER: small bug in ambmask (amber9) Kateryna Miroshnychenko (Mon Jul 10 2006 - 07:53:02 PDT)
- AMBER: program to calculate net charge of a ligand for Antechamber Christophe Guilbert (Mon Jul 10 2006 - 18:30:39 PDT)
- AMBER: Question about NSCM Xiaowei (David) Li (Tue Jul 11 2006 - 01:25:48 PDT)
- AMBER: Amber 8.0 no numerical value and offset for the predicted pKa of many titrable residue!! Guillaume Bollot (Tue Jul 11 2006 - 04:19:29 PDT)
- AMBER: Amber crashed due to power surge and giving problems.. Gobind Bisht (Tue Jul 11 2006 - 07:46:54 PDT)
- AMBER: Ptraj: Hbond time series Zu Thur Yew (Tue Jul 11 2006 - 08:19:34 PDT)
- AMBER: applying restraints on pre-defined planes Vlad Cojocaru (Tue Jul 11 2006 - 08:34:07 PDT)
- AMBER: problem about Distance Restraints. Qingning Shu (Tue Jul 11 2006 - 20:38:48 PDT)
- AMBER: iso command and a cubic box Patricia Hunt (Wed Jul 12 2006 - 00:03:03 PDT)
- AMBER: Where is the repulsion energy ( part of nonpolar solvation energy) in MM_PBSA ? Changge Ji (Tue Jul 11 2006 - 23:03:30 PDT)
- AMBER: simulate a self-assemble process in vacuum Eric Hu (Wed Jul 12 2006 - 16:22:58 PDT)
- AMBER: Antechamber 1.26 is released Junmei Wang (Wed Jul 12 2006 - 16:42:32 PDT)
- AMBER: Etot has downward drift in 'NVE' ensemble John S. Zintsmaster (Wed Jul 12 2006 - 19:01:08 PDT)
- AMBER: Free energy calculated from mm_pbsa gtg549i.mail.gatech.edu (Thu Jul 13 2006 - 00:26:44 PDT)
- AMBER: New (small) Topology without solvent from previous one (big) with solvent j j (Thu Jul 13 2006 - 03:50:55 PDT)
- AMBER: New (small) Topology without solvent from previous one (big) with solvent j j (Thu Jul 13 2006 - 03:47:15 PDT)
- AMBER: Ringof dna Flora Mactavish (Thu Jul 13 2006 - 06:14:22 PDT)
- AMBER: center molecule using iwrap=1? Gustavo Seabra (Thu Jul 13 2006 - 11:21:17 PDT)
- AMBER: QMMM simulation amit.mbu.iisc.ernet.in (Thu Jul 13 2006 - 11:38:48 PDT)
- AMBER: Replica exchange with Amber9 Atsutoshi Okabe (Thu Jul 13 2006 - 23:20:21 PDT)
- AMBER: Amber 8 on Rocks 4, Opteron, PGI 6.1 Lars Packschies (Fri Jul 14 2006 - 03:18:08 PDT)
- RE: AMBER: Compiling / Installing Amber 8 on SUSE 10.1 hayden (Fri Jul 14 2006 - 03:27:54 PDT)
- Re: AMBER: Compiling / Installing Amber 8 on SUSE 10.1 Andreas Svrcek-Seiler (Fri Jul 14 2006 - 03:38:10 PDT)
- AMBER: Compiling Leap problem sethl.gatech.edu (Fri Jul 14 2006 - 14:36:38 PDT)
- AMBER: amber9 Piotr Cieplak (Fri Jul 14 2006 - 15:02:36 PDT)
- AMBER: Amber 9 installation issues Glass, Kevin A (Fri Jul 14 2006 - 16:18:36 PDT)
- AMBER: "noimage" option for radial distribution functions Ozlem Demir (Sun Jul 16 2006 - 14:14:31 PDT)
- AMBER: Amber 8.0 MM_PBSA Stability : question about methodology Guillaume Bollot (Mon Jul 17 2006 - 05:18:41 PDT)
- AMBER: Replica exchange Austin B. Yongye (Mon Jul 17 2006 - 05:31:09 PDT)
- AMBER: RMS & PCA Zu Thur Yew (Mon Jul 17 2006 - 07:55:12 PDT)
- AMBER: Obtaining LCPO parameters for F and Fe zachary hartman (Mon Jul 17 2006 - 11:16:54 PDT)
- Re: AMBER: Creating an Intercalation site Bill Ross (Mon Jul 17 2006 - 12:49:20 PDT)
- AMBER: PMEMD with NMR restraint and position restraint Ting Wang (Mon Jul 17 2006 - 16:18:31 PDT)
- Re: AMBER: Creating an Intercalation site Thomas Cheatham (Mon Jul 17 2006 - 13:13:54 PDT)
- AMBER: Dynamics and Restraint problem Andrew Box (Mon Jul 17 2006 - 16:49:51 PDT)
- AMBER: water diffusion Sergei Smirnov (Mon Jul 17 2006 - 17:48:59 PDT)
- AMBER: PhosphoThreonine Parms for use with ff03 Zu Thur Yew (Mon Jul 17 2006 - 22:19:15 PDT)
- AMBER: Calculating energy for specific part of system Adam Pelzer (Tue Jul 18 2006 - 15:32:34 PDT)
- AMBER: Replica exchange Austin B. Yongye (Wed Jul 19 2006 - 08:04:44 PDT)
- AMBER: Long line of input Myunggi Yi (Wed Jul 19 2006 - 13:13:26 PDT)
- AMBER: difficulties with antechamber: tests dont even run frustrated modeller (Wed Jul 19 2006 - 16:06:36 PDT)
- AMBER: Myrinet or Gigabit ethernet? Mingfeng Yang (Thu Jul 20 2006 - 06:35:08 PDT)
- AMBER: Failure of iwrap in PMEMD Myunggi Yi (Thu Jul 20 2006 - 07:01:07 PDT)
- AMBER: Gb Na+ ions DNA Conn O'Rourke (Thu Jul 20 2006 - 08:16:05 PDT)
- Re: AMBER: ptraj help - amber7 failed, amber8 read prmtop file incorrectly... fine wu (Thu Jul 20 2006 - 08:55:55 PDT)
- AMBER: saltcon variable Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu Jul 20 2006 - 12:00:01 PDT)
- AMBER: PDB from .rst? Evan Kelly (Thu Jul 20 2006 - 13:51:09 PDT)
- AMBER: Replica Exchange Austin B. Yongye (Thu Jul 20 2006 - 19:07:46 PDT)
- AMBER: Modelling dsDNA less than 10bp Lena Dolghih (Fri Jul 21 2006 - 06:15:16 PDT)
- AMBER: combining different versions of AMBER Melissa Foley (Fri Jul 21 2006 - 12:25:35 PDT)
- AMBER: Silicon related parameters hbluo (Sat Jul 22 2006 - 10:52:17 PDT)
- AMBER: Simulating an "average" DNA sequence S. Jamal Rahi (Fri Jul 21 2006 - 20:20:36 PDT)
- AMBER: problems of running sander.MPI of amber9 on remote node Chengwen Chen (Sun Jul 23 2006 - 23:29:20 PDT)
- AMBER: AMBER9 netcdf trajectory with VMD 1.8.4 Fabian Boes (Mon Jul 24 2006 - 01:01:46 PDT)
- AMBER: How to resume remaining simulation pkb bioinfo (Mon Jul 24 2006 - 03:05:23 PDT)
- AMBER: Minimization problem: coordinates out of virtual box Zu Thur Yew (Mon Jul 24 2006 - 05:53:19 PDT)
- AMBER: Tutorial 8, section 6: best fit before clustering sangeeta (Mon Jul 24 2006 - 06:18:05 PDT)
- AMBER: library for 8oxoguanine Carra, Claudio \(JSC-SK\)[USRA] (Mon Jul 24 2006 - 12:50:59 PDT)
- AMBER: Building an RNA - Proflavin Complex sethl.gatech.edu (Mon Jul 24 2006 - 13:05:49 PDT)
- AMBER: Confusion re AMBER SMD output Alik Widge (Mon Jul 24 2006 - 13:31:34 PDT)
- AMBER: process_mdout.perl's output is empty Prashanth Athri (Mon Jul 24 2006 - 13:53:04 PDT)
- Re: [Fwd: AMBER: Long line of input] Myunggi Yi (Tue Jul 25 2006 - 09:08:27 PDT)
- AMBER: Hybridization in leap opitz.che.udel.edu (Tue Jul 25 2006 - 11:23:12 PDT)
- AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap Lwin, ThuZar (Tue Jul 25 2006 - 17:39:32 PDT)
- AMBER: parallel installation of amber8 on HP cluster Manish Datt (Wed Jul 26 2006 - 03:00:30 PDT)
- AMBER: leap error AYTUG TUNCEL (Wed Jul 26 2006 - 16:29:35 PDT)
- AMBER: Harmonic restraint along z-axis Myunggi Yi (Wed Jul 26 2006 - 17:26:02 PDT)
- AMBER: dummy atoms in MMPBSA Andrea Bortolato (Thu Jul 27 2006 - 01:10:50 PDT)
- AMBER: xleap Md Jahidul Islam (Thu Jul 27 2006 - 02:49:36 PDT)
- AMBER: Can't open xleap Jahidul Islam (Thu Jul 27 2006 - 03:16:08 PDT)
- AMBER: Zinc parameters Nitin Bhardwaj (Thu Jul 27 2006 - 09:35:57 PDT)
- AMBER: Correction on Zinc parameters Nitin Bhardwaj (Thu Jul 27 2006 - 09:38:00 PDT)
- AMBER: Zinc-coordinating histidine protonation state Nitin Bhardwaj (Thu Jul 27 2006 - 13:01:16 PDT)
- AMBER: Zinc coordinating CYS Nitin Bhardwaj (Thu Jul 27 2006 - 14:30:45 PDT)
- RE: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap. . Lwin, ThuZar (Thu Jul 27 2006 - 18:35:19 PDT)
- AMBER: Ken Merz (Sat Jul 29 2006 - 08:28:53 PDT)
- AMBER: Having trouble with Nucgen for generating pdb more than 16 bps amit.mbu.iisc.ernet.in (Sun Jul 30 2006 - 11:51:05 PDT)
- Re: AMBER: Having trouble with Nucgen for generating pdb more than 16 bps Bill Ross (Mon Jul 31 2006 - 11:53:11 PDT)
- AMBER: loading torsion parameters Nitin Bhardwaj (Mon Jul 31 2006 - 12:47:19 PDT)
- Re: AMBER: loading torsion parameters Bill Ross (Mon Jul 31 2006 - 13:49:38 PDT)
- AMBER: For different ligand conformation pkb bioinfo (Mon Jul 31 2006 - 06:53:45 PDT)
- AMBER: Using a trajectory and some PDB files as input for PCA Zu Thur Yew (Mon Jul 31 2006 - 03:20:42 PDT)
- AMBER: Distance between two regions Baker, Bo-Yang (Mon Jul 31 2006 - 17:16:02 PDT)
- AMBER: from traj to crd Fabián Alejandro Rodríguez (Mon Jul 31 2006 - 17:58:19 PDT)
- Last message date: Wed Aug 02 2006 - 06:07:09 PDT
- Archived on: Wed Mar 17 2010 - 06:00:44 PDT
