AMBER Archive (2008) - Jun 2008 By ThreadMost recent messages
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About this archive
Starting: Sun Jun 01 2008 - 02:12:12 CDT
Ending: Mon Jun 30 2008 - 17:46:45 CDT
- AMBER: PCA - analysis Ibrahim Moustafa (Sun Jun 01 2008 - 13:00:35 CDT)
- Fw: RE: AMBER: SANDER and PMEMD with openmpi. NO MORE failure 'make test.pmemd' Francesco Pietra (Mon Jun 02 2008 - 05:22:38 CDT)
- AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 Jarrod Smith (Mon Jun 02 2008 - 11:43:24 CDT)
- AMBER: VMD file generation 4 - mdcrd ptraj analysis Campbell, Patrick (Mon Jun 02 2008 - 13:26:15 CDT)
- AMBER: VMD file generation 4 - mdcrd analysis Campbell, Patrick (Mon Jun 02 2008 - 15:21:00 CDT)
- AMBER: PCA analysis Ibrahim Moustafa (Mon Jun 02 2008 - 16:09:17 CDT)
- AMBER: Missing gaff angle parameters for dimethyl esters Lin, Pohan (Mon Jun 02 2008 - 16:20:24 CDT)
- AMBER: corrupted restart file yavuzturkm_at_prc.boun.edu.tr (Tue Jun 03 2008 - 04:18:25 CDT)
- AMBER: Temperature controlling method in AMBER tinni sona (Tue Jun 03 2008 - 04:43:11 CDT)
- AMBER: solvate box : buffer list fatima.chami_at_durham.ac.uk (Tue Jun 03 2008 - 12:51:55 CDT)
- AMBER: How to calculate RMSIP after PCA analysis by PTRAJ? sychen (Wed Jun 04 2008 - 07:27:45 CDT)
- AMBER: problems with sleap Alan (Wed Jun 04 2008 - 10:40:04 CDT)
- AMBER: NMODE units and hrmax value for Langevine modes Yang, Lee-Wei (Wed Jun 04 2008 - 11:27:00 CDT)
- AMBER: amber installation on cluster Pankaj R. Daga (Wed Jun 04 2008 - 12:27:57 CDT)
- AMBER: NAB documentation for programmers ramu_at_vt.edu (Wed Jun 04 2008 - 13:59:27 CDT)
- AMBER: ptraj imaging issue Vlad Cojocaru (Wed Jun 04 2008 - 14:07:44 CDT)
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Thu Jun 05 2008 - 00:27:39 CDT)
- AMBER: problem of install amber9 Xioling Chuang (Thu Jun 05 2008 - 03:37:27 CDT)
- AMBER: Free energy of dissociation fatima.chami_at_durham.ac.uk (Thu Jun 05 2008 - 07:02:43 CDT)
- AMBER: NAN errors in Etot, EPtot, EKtot and EELEC Praveena Gopal (Thu Jun 05 2008 - 07:04:00 CDT)
- AMBER: netcdf configure returned 1 Jens Lattig (Thu Jun 05 2008 - 08:46:45 CDT)
- AMBER: netcdf configure returned 1 - PROBLEM SOLVED Jens Lattig (Thu Jun 05 2008 - 09:42:03 CDT)
- AMBER: A problem of installing Amber10 Yicun Ni (Thu Jun 05 2008 - 10:55:53 CDT)
- AMBER: Nmode - entropy calculation of receptor - should I apply restraint? Seth Lilavivat (Thu Jun 05 2008 - 12:03:08 CDT)
- AMBER: RE: solvating RNA in 8M urea box Ross Walker (Thu Jun 05 2008 - 19:12:42 CDT)
- AMBER: Query on MM-PBSA Neha Gandhi (Fri Jun 06 2008 - 00:46:32 CDT)
- AMBER: PROBLEM: AmberTools Installation using Ubuntu Jens Lattig (Fri Jun 06 2008 - 03:13:06 CDT)
- AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Ian (Fri Jun 06 2008 - 04:19:58 CDT)
- AMBER: Problem While Installing Amber Ranga Swamy (Fri Jun 06 2008 - 04:34:17 CDT)
- AMBER: VMD Movie .mdcrd file ptraj Campbell, Patrick (Fri Jun 06 2008 - 08:22:50 CDT)
- AMBER: NAB documentation David Case (Fri Jun 06 2008 - 11:24:44 CDT)
- Re:AMBER:VMD Movie.mdcrd Campbell, Patrick (Fri Jun 06 2008 - 13:56:52 CDT)
- AMBER: 100 short MD runs within a single Sander script? Sebastian Stolzenberg (Fri Jun 06 2008 - 23:55:37 CDT)
- AMBER: Combine mdcrd while stripping WAT problem Francesco Pietra (Sun Jun 08 2008 - 10:40:07 CDT)
- AMBER: problem in starting sander Qiuting Hong (Sun Jun 08 2008 - 13:25:43 CDT)
- AMBER: MM-PBSA and delphi Neha Gandhi (Mon Jun 09 2008 - 00:49:54 CDT)
- AMBER: Calcium and Magnesium LJ parameters Daniel Smith (Mon Jun 09 2008 - 18:02:28 CDT)
- AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating xiaonan zhang (Tue Jun 10 2008 - 07:24:02 CDT)
- AMBER: SMD pulling velocity fatima.chami_at_durham.ac.uk (Tue Jun 10 2008 - 09:06:38 CDT)
- AMBER: how to calculate the interaction energy Wang,Ying (Tue Jun 10 2008 - 09:52:10 CDT)
- AMBER: Simulating complexes with magnesium atoms Sasha Buzko (Tue Jun 10 2008 - 16:32:13 CDT)
- AMBER: box shape changed at NVT fatima.chami_at_durham.ac.uk (Wed Jun 11 2008 - 09:25:09 CDT)
- AMBER: sander.MPI / openmpi on PBS Arturas Ziemys (Wed Jun 11 2008 - 13:59:52 CDT)
- AMBER: 2D RMS plot Steve Spronk (Wed Jun 11 2008 - 14:18:32 CDT)
- AMBER: Coordinated Zinc Khaled Barakat (Wed Jun 11 2008 - 14:29:18 CDT)
- AMBER: Antechamber and topology file TAEJIN KIM (Wed Jun 11 2008 - 18:05:14 CDT)
- AMBER: updating documentation Alan (Thu Jun 12 2008 - 04:52:40 CDT)
- AMBER: using Velocity-Verlet algorithm oguz gurbulak (Thu Jun 12 2008 - 07:07:20 CDT)
- AMBER: anisotropic pressure scaling ntp=2 fatima.chami_at_durham.ac.uk (Thu Jun 12 2008 - 08:18:13 CDT)
- AMBER: SMD RESTRAINTS fatima.chami_at_durham.ac.uk (Thu Jun 12 2008 - 11:23:00 CDT)
- AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell (Thu Jun 12 2008 - 11:31:03 CDT)
- AMBER: Sander crashes >99999 atoms plmallip_at_mail.uh.edu (Thu Jun 12 2008 - 18:26:57 CDT)
- AMBER: PCAL and polar contribution in the output file Neha Gandhi (Fri Jun 13 2008 - 00:42:54 CDT)
- AMBER: amber10 make fails for static/parallel James W. Caldwell (Fri Jun 13 2008 - 17:50:19 CDT)
- AMBER: Ewald error estimate Pavan G (Sun Jun 15 2008 - 09:22:48 CDT)
- AMBER: Problem with running refinement of NMR structures with RDCs Qi Zhang (Sun Jun 15 2008 - 15:20:21 CDT)
- AMBER: Eigenmode dynamics in Ptraj fatima.chami_at_durham.ac.uk (Mon Jun 16 2008 - 07:59:42 CDT)
- AMBER: the SPCFW water model Vlad Cojocaru (Mon Jun 16 2008 - 11:19:34 CDT)
- AMBER: sander.MPI / parallel Arturas Ziemys (Mon Jun 16 2008 - 12:00:34 CDT)
- AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez (Mon Jun 16 2008 - 09:31:12 CDT)
- AMBER: about resp charges WanJ Ding (Mon Jun 16 2008 - 14:44:55 CDT)
- AMBER: IRED to time correlation fatima.chami_at_durham.ac.uk (Mon Jun 16 2008 - 15:25:22 CDT)
- AMBER: program to calculate rmsd rams rams (Mon Jun 16 2008 - 21:28:24 CDT)
- AMBER: How to solve - Missing BELE for MM in 1 in amber. Thomas Leonard (Mon Jun 16 2008 - 22:05:59 CDT)
- AMBER: How to solve - Missing BELE for MM in 1 in amber. Thomas Leonard (Mon Jun 16 2008 - 22:06:01 CDT)
- AMBER: improving GAFF sulfonamide parameters Floris Buelens (Tue Jun 17 2008 - 04:57:46 CDT)
- AMBER: ligand complexed simulation Siddharth Rastogi (Tue Jun 17 2008 - 05:56:15 CDT)
- AMBER: suggestion for next amberTools 1.1 Alan (Tue Jun 17 2008 - 06:01:06 CDT)
- AMBER: "Dumping RAW 2D RMS data is not yet implemented"? Steve Spronk (Tue Jun 17 2008 - 09:00:08 CDT)
- AMBER: to understand GAFF: about A and B coefficients Alan (Tue Jun 17 2008 - 11:42:34 CDT)
- AMBER: multiple dihedral restraints using group (in Amber 10) mkseo (Tue Jun 17 2008 - 16:00:50 CDT)
- AMBER: MM-PBSA Neha Gandhi (Wed Jun 18 2008 - 02:37:33 CDT)
- AMBER: Eigenmode dynamics - imaging traj fatima.chami_at_durham.ac.uk (Wed Jun 18 2008 - 05:09:26 CDT)
- AMBER: about gaff.dat in ambeTools 1.0 Alan (Wed Jun 18 2008 - 09:44:02 CDT)
- AMBER: ptraj fatima.chami_at_durham.ac.uk (Wed Jun 18 2008 - 10:21:50 CDT)
- AMBER: cross correlation function using iRED matrix fatima.chami_at_durham.ac.uk (Wed Jun 18 2008 - 12:07:25 CDT)
- AMBER: tip3p water and shake Wang,Ying (Wed Jun 18 2008 - 15:07:13 CDT)
- AMBER: sp carbon notation? Laura Benton (Wed Jun 18 2008 - 18:16:35 CDT)
- AMBER: questions about gaff yzhao (Wed Jun 18 2008 - 21:01:45 CDT)
- AMBER: [Fwd: failure to load box parameters] Daniel Smith (Wed Jun 18 2008 - 22:58:10 CDT)
- AMBER: How to create average structure? Shen, Lingling (Wed Jun 18 2008 - 23:44:03 CDT)
- AMBER: how to extract x,y,z of a set of atoms from an MD trajectories fatima.chami_at_durham.ac.uk (Thu Jun 19 2008 - 04:16:52 CDT)
- AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge) (Thu Jun 19 2008 - 05:22:53 CDT)
- AMBER: Installation Problem of AMBER10 bhargav patel (Thu Jun 19 2008 - 05:57:26 CDT)
- AMBER: How to extract solvent box information from .rst or .mdcrd files? Panwang Zhou (Thu Jun 19 2008 - 09:13:18 CDT)
- AMBER: simple sander James W. Caldwell (Thu Jun 19 2008 - 18:30:39 CDT)
- AMBER: ligand complexed simulation Siddharth Rastogi (Fri Jun 20 2008 - 02:14:18 CDT)
- AMBER: GAFF for organic crystals Rabone, Jeremy (Fri Jun 20 2008 - 03:05:18 CDT)
- AMBER: rdparm help Alan (Fri Jun 20 2008 - 06:12:17 CDT)
- AMBER: AmberTools 1.0 installation error: x86_64 Matthew Danielson (Fri Jun 20 2008 - 10:44:21 CDT)
- AMBER: Amber 10 timing Ed Pate (Fri Jun 20 2008 - 12:08:37 CDT)
- AMBER: SIZE.h problems Å·ÑôµÂ·½ (Sat Jun 21 2008 - 07:33:49 CDT)
- AMBER: (no subject) Daniel B. Kaplan (Sun Jun 22 2008 - 18:46:17 CDT)
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Mon Jun 23 2008 - 00:07:34 CDT)
- AMBER: How to adjust the problem of "Vlimit exceeded" Biman Jana (Mon Jun 23 2008 - 02:28:27 CDT)
- AMBER: How to confirm atom types of small molecule perceived by antechamber xiaonan zhang (Mon Jun 23 2008 - 03:39:30 CDT)
- AMBER: source of AMBER9 Germain Vallverdu (Mon Jun 23 2008 - 09:09:29 CDT)
- AMBER: amber10/dat/leap/cmd/README need update Alan (Mon Jun 23 2008 - 09:59:21 CDT)
- AMBER: Antechamber Question Daniel B. Kaplan (Mon Jun 23 2008 - 11:51:28 CDT)
- AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
- AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
- AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
- AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
- AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
- AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
- AMBER: dihedral energy calculation inconsistent with gaussian's result Q733 (Mon Jun 23 2008 - 21:43:36 CDT)
- AMBER: unsubscribe amber sanket.deshmukh_at_ucd.ie (Tue Jun 24 2008 - 06:07:42 CDT)
- AMBER: A-prime RNA input file Å·ÑôµÂ·½ (Tue Jun 24 2008 - 06:16:27 CDT)
- AMBER: qmmm_DFTB problem Dr. Xiaofeng (Frank) Duan (Tue Jun 24 2008 - 08:58:46 CDT)
- AMBER: Compilation of amber8 patched with ramd Francesco Pietra (Tue Jun 24 2008 - 09:32:54 CDT)
- AMBER: dihedral potential with odd periodicity Germain Vallverdu (Tue Jun 24 2008 - 09:43:26 CDT)
- AMBER: Using AMBER forces Steven Winfield (Tue Jun 24 2008 - 10:44:41 CDT)
- AMBER: rdparm Segmentation fault on Ubuntu Alan (Tue Jun 24 2008 - 10:50:12 CDT)
- AMBER: how to derive torsional angle parameters in gaff Junmei Wang (Tue Jun 24 2008 - 20:45:42 CDT)
- AMBER: Debugf AMBER9 John Palmeri (Wed Jun 25 2008 - 02:38:53 CDT)
- AMBER: TI calculations in Amber10 Samuel Genheden (a03samge) (Wed Jun 25 2008 - 06:58:28 CDT)
- AMBER: A problem of dihedral angle Harry (Yicun) Ni (Wed Jun 25 2008 - 10:31:24 CDT)
- AMBER: amber10 compile gfortran question James W. Caldwell (Wed Jun 25 2008 - 13:10:58 CDT)
- AMBER: sleap - TER-card In Hee Park (Wed Jun 25 2008 - 14:14:39 CDT)
- AMBER: rdparm Segmentation fault Alan (Wed Jun 25 2008 - 16:24:34 CDT)
- AMBER: Antechamber/mopac am1-bcc charge Dong Xu (Wed Jun 25 2008 - 17:09:39 CDT)
- AMBER: (no subject) Daniel B. Kaplan (Wed Jun 25 2008 - 21:23:43 CDT)
- AMBER: Amber:unsubscribe amber sanket.deshmukh_at_ucd.ie (Thu Jun 26 2008 - 06:53:22 CDT)
- AMBER: concerning force fields Adrien Delmont (Thu Jun 26 2008 - 10:14:15 CDT)
- AMBER: Peseckis, Steven M. (Thu Jun 26 2008 - 10:54:05 CDT)
- AMBER: ligand partial charge and conformation question Dong Xu (Thu Jun 26 2008 - 13:01:31 CDT)
- AMBER: output file AMBER9_MPI Vijay Manickam Achari (Thu Jun 26 2008 - 14:06:19 CDT)
- AMBER: Dihedral Angle Parameters Ilyas Yildirim (Thu Jun 26 2008 - 16:07:16 CDT)
- AMBER: REMD Amber10 : error in reading namelist cntrl rebeca (Fri Jun 27 2008 - 04:01:26 CDT)
- AMBER: Group specification problem fatima.chami_at_durham.ac.uk (Fri Jun 27 2008 - 07:59:09 CDT)
- AMBER: pmemd 10 output Vlad Cojocaru (Fri Jun 27 2008 - 10:48:35 CDT)
- AMBER: Test scripts James W. Caldwell (Fri Jun 27 2008 - 11:35:26 CDT)
- AMBER: ptraj - read in part of trajectory Seth Lilavivat (Fri Jun 27 2008 - 11:41:51 CDT)
- AMBER: question about the charge Harry (Yicun) Ni (Fri Jun 27 2008 - 15:37:55 CDT)
- AMBER: Seed for random number generator Francesco Pietra (Sun Jun 29 2008 - 03:22:12 CDT)
- AMBER: Constrained group fatima.chami_at_durham.ac.uk (Mon Jun 30 2008 - 04:54:02 CDT)
- AMBER: NMR refinement teresa.ierano_at_unina.it (Mon Jun 30 2008 - 05:37:48 CDT)
- AMBER: nmode analysis Joachim Reichelt (Mon Jun 30 2008 - 06:53:21 CDT)
- AMBER: hold atoms fixed Boutheina Kerkeni (Mon Jun 30 2008 - 07:51:17 CDT)
- AMBER: wrapping a restart file fatima.chami_at_durham.ac.uk (Mon Jun 30 2008 - 09:40:58 CDT)
- AMBER: (no subject) fatima.chami_at_durham.ac.uk (Mon Jun 30 2008 - 11:26:23 CDT)
- AMBER: watershell cero? rebeca (Mon Jun 30 2008 - 11:22:11 CDT)
- AMBER: MM-PBSA calculation problem Wei Huang (Mon Jun 30 2008 - 11:41:16 CDT)
- AMBER: error in reading namelist cntrl Maria Frushicheva (Mon Jun 30 2008 - 15:02:50 CDT)
- AMBER: Regarding force field ff02 and ion library Abhishek Singh (Mon Jun 30 2008 - 15:54:52 CDT)
- AMBER: missing torsion parameters John Bennett (Mon Jun 30 2008 - 16:06:07 CDT)
Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:47 CST
508 messages sorted by:
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