Amber Archive Jun 2008 by thread
- RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Francesco Pietra (Sun Jun 01 2008 - 00:12:12 PDT)
- AMBER: PCA - analysis Ibrahim Moustafa (Sun Jun 01 2008 - 11:00:35 PDT)
- Fw: RE: AMBER: SANDER and PMEMD with openmpi. NO MORE failure 'make test.pmemd' Francesco Pietra (Mon Jun 02 2008 - 03:22:38 PDT)
- AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 Jarrod Smith (Mon Jun 02 2008 - 09:43:24 PDT)
- Re: AMBER: ptraj has trouble with x-plor psf file from VMD Jufang Shan (Mon Jun 02 2008 - 08:52:28 PDT)
- Re: AMBER: Jarzynski David Mobley (Mon Jun 02 2008 - 10:25:16 PDT)
- AMBER: VMD file generation 4 - mdcrd ptraj analysis Campbell, Patrick (Mon Jun 02 2008 - 11:26:15 PDT)
- AMBER: VMD file generation 4 - mdcrd analysis Campbell, Patrick (Mon Jun 02 2008 - 13:21:00 PDT)
- AMBER: PCA analysis Ibrahim Moustafa (Mon Jun 02 2008 - 14:09:17 PDT)
- AMBER: Missing gaff angle parameters for dimethyl esters Lin, Pohan (Mon Jun 02 2008 - 14:20:24 PDT)
- Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error David A. Case (Mon Jun 02 2008 - 16:23:46 PDT)
- Re: AMBER: gasteiger is not working with ambertools 1.0 David A. Case (Mon Jun 02 2008 - 17:12:55 PDT)
- AMBER: corrupted restart file yavuzturkm.prc.boun.edu.tr (Tue Jun 03 2008 - 02:18:25 PDT)
- AMBER: Temperature controlling method in AMBER tinni sona (Tue Jun 03 2008 - 02:43:11 PDT)
- AMBER: solvate box : buffer list fatima.chami.durham.ac.uk (Tue Jun 03 2008 - 10:51:55 PDT)
- Re: AMBER: drawing repeated units Taufik Al-Sarraj (Tue Jun 03 2008 - 15:25:59 PDT)
- AMBER: problems with sleap Alan (Wed Jun 04 2008 - 08:40:04 PDT)
- AMBER: How to calculate RMSIP after PCA analysis by PTRAJ? sychen (Wed Jun 04 2008 - 05:27:45 PDT)
- AMBER: NMODE units and hrmax value for Langevine modes Yang, Lee-Wei (Wed Jun 04 2008 - 09:27:00 PDT)
- AMBER: amber installation on cluster Pankaj R. Daga (Wed Jun 04 2008 - 10:27:57 PDT)
- AMBER: NAB documentation for programmers ramu.vt.edu (Wed Jun 04 2008 - 11:59:27 PDT)
- AMBER: ptraj imaging issue Vlad Cojocaru (Wed Jun 04 2008 - 12:07:44 PDT)
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Wed Jun 04 2008 - 22:27:39 PDT)
- AMBER: problem of install amber9 Xioling Chuang (Thu Jun 05 2008 - 01:37:27 PDT)
- AMBER: NAN errors in Etot, EPtot, EKtot and EELEC Praveena Gopal (Thu Jun 05 2008 - 05:04:00 PDT)
- AMBER: Free energy of dissociation fatima.chami.durham.ac.uk (Thu Jun 05 2008 - 05:02:43 PDT)
- AMBER: netcdf configure returned 1 Jens Lattig (Thu Jun 05 2008 - 06:46:45 PDT)
- AMBER: netcdf configure returned 1 - PROBLEM SOLVED Jens Lattig (Thu Jun 05 2008 - 07:42:03 PDT)
- AMBER: A problem of installing Amber10 Yicun Ni (Thu Jun 05 2008 - 08:55:53 PDT)
- AMBER: Nmode - entropy calculation of receptor - should I apply restraint? Seth Lilavivat (Thu Jun 05 2008 - 10:03:08 PDT)
- AMBER: RE: solvating RNA in 8M urea box Ross Walker (Thu Jun 05 2008 - 17:12:42 PDT)
- AMBER: Query on MM-PBSA Neha Gandhi (Thu Jun 05 2008 - 22:46:32 PDT)
- AMBER: PROBLEM: AmberTools Installation using Ubuntu Jens Lattig (Fri Jun 06 2008 - 01:13:06 PDT)
- AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Ian (Fri Jun 06 2008 - 02:19:58 PDT)
- AMBER: Problem While Installing Amber Ranga Swamy (Fri Jun 06 2008 - 02:34:17 PDT)
- AMBER: VMD Movie .mdcrd file ptraj Campbell, Patrick (Fri Jun 06 2008 - 06:22:50 PDT)
- AMBER: NAB documentation David Case (Fri Jun 06 2008 - 09:24:44 PDT)
- Re:AMBER:VMD Movie.mdcrd Campbell, Patrick (Fri Jun 06 2008 - 11:56:52 PDT)
- AMBER: 100 short MD runs within a single Sander script? Sebastian Stolzenberg (Fri Jun 06 2008 - 21:55:37 PDT)
- AMBER: Combine mdcrd while stripping WAT problem Francesco Pietra (Sun Jun 08 2008 - 08:40:07 PDT)
- AMBER: problem in starting sander Qiuting Hong (Sun Jun 08 2008 - 11:25:43 PDT)
- AMBER: MM-PBSA and delphi Neha Gandhi (Sun Jun 08 2008 - 22:49:54 PDT)
- AMBER: Calcium and Magnesium LJ parameters Daniel Smith (Mon Jun 09 2008 - 16:02:28 PDT)
- AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating xiaonan zhang (Tue Jun 10 2008 - 05:24:02 PDT)
- AMBER: SMD pulling velocity fatima.chami.durham.ac.uk (Tue Jun 10 2008 - 07:06:38 PDT)
- AMBER: how to calculate the interaction energy Wang,Ying (Tue Jun 10 2008 - 07:52:10 PDT)
- AMBER: Simulating complexes with magnesium atoms Sasha Buzko (Tue Jun 10 2008 - 14:32:13 PDT)
- AMBER: box shape changed at NVT fatima.chami.durham.ac.uk (Wed Jun 11 2008 - 07:25:09 PDT)
- AMBER: sander.MPI / openmpi on PBS Arturas Ziemys (Wed Jun 11 2008 - 11:59:52 PDT)
- AMBER: 2D RMS plot Steve Spronk (Wed Jun 11 2008 - 12:18:32 PDT)
- AMBER: Antechamber and topology file TAEJIN KIM (Wed Jun 11 2008 - 16:05:14 PDT)
- AMBER: Coordinated Zinc Khaled Barakat (Wed Jun 11 2008 - 12:29:18 PDT)
- AMBER: updating documentation Alan (Thu Jun 12 2008 - 02:52:40 PDT)
- AMBER: using Velocity-Verlet algorithm oguz gurbulak (Thu Jun 12 2008 - 05:07:20 PDT)
- AMBER: anisotropic pressure scaling ntp=2 fatima.chami.durham.ac.uk (Thu Jun 12 2008 - 06:18:13 PDT)
- AMBER: SMD RESTRAINTS fatima.chami.durham.ac.uk (Thu Jun 12 2008 - 09:23:00 PDT)
- AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell (Thu Jun 12 2008 - 09:31:03 PDT)
- Re: AMBER: potassium ion Lars Skjærven (Thu Jun 12 2008 - 10:46:36 PDT)
- AMBER: Sander crashes >99999 atoms plmallip.mail.uh.edu (Thu Jun 12 2008 - 16:26:57 PDT)
- AMBER: PCAL and polar contribution in the output file Neha Gandhi (Thu Jun 12 2008 - 22:42:54 PDT)
- AMBER: amber10 make fails for static/parallel James W. Caldwell (Fri Jun 13 2008 - 15:50:19 PDT)
- AMBER: Ewald error estimate Pavan G (Sun Jun 15 2008 - 07:22:48 PDT)
- AMBER: Problem with running refinement of NMR structures with RDCs Qi Zhang (Sun Jun 15 2008 - 13:20:21 PDT)
- AMBER: Eigenmode dynamics in Ptraj fatima.chami.durham.ac.uk (Mon Jun 16 2008 - 05:59:42 PDT)
- AMBER: the SPCFW water model Vlad Cojocaru (Mon Jun 16 2008 - 09:19:34 PDT)
- AMBER: sander.MPI / parallel Arturas Ziemys (Mon Jun 16 2008 - 10:00:34 PDT)
- AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez (Mon Jun 16 2008 - 07:31:12 PDT)
- AMBER: about resp charges WanJ Ding (Mon Jun 16 2008 - 12:44:55 PDT)
- AMBER: IRED to time correlation fatima.chami.durham.ac.uk (Mon Jun 16 2008 - 13:25:22 PDT)
- AMBER: program to calculate rmsd rams rams (Mon Jun 16 2008 - 19:28:24 PDT)
- AMBER: How to solve - Missing BELE for MM in 1 in amber. Thomas Leonard (Mon Jun 16 2008 - 20:05:59 PDT)
- AMBER: How to solve - Missing BELE for MM in 1 in amber. Thomas Leonard (Mon Jun 16 2008 - 20:06:01 PDT)
- AMBER: improving GAFF sulfonamide parameters Floris Buelens (Tue Jun 17 2008 - 02:57:46 PDT)
- AMBER: ligand complexed simulation Siddharth Rastogi (Tue Jun 17 2008 - 03:56:15 PDT)
- AMBER: suggestion for next amberTools 1.1 Alan (Tue Jun 17 2008 - 04:01:06 PDT)
- AMBER: "Dumping RAW 2D RMS data is not yet implemented"? Steve Spronk (Tue Jun 17 2008 - 07:00:08 PDT)
- AMBER: to understand GAFF: about A and B coefficients Alan (Tue Jun 17 2008 - 09:42:34 PDT)
- AMBER: multiple dihedral restraints using group (in Amber 10) mkseo (Tue Jun 17 2008 - 14:00:50 PDT)
- AMBER: MM-PBSA Neha Gandhi (Wed Jun 18 2008 - 00:37:33 PDT)
- AMBER: Eigenmode dynamics - imaging traj fatima.chami.durham.ac.uk (Wed Jun 18 2008 - 03:09:26 PDT)
- AMBER: about gaff.dat in ambeTools 1.0 Alan (Wed Jun 18 2008 - 07:44:02 PDT)
- AMBER: ptraj fatima.chami.durham.ac.uk (Wed Jun 18 2008 - 08:21:50 PDT)
- AMBER: cross correlation function using iRED matrix fatima.chami.durham.ac.uk (Wed Jun 18 2008 - 10:07:25 PDT)
- AMBER: tip3p water and shake Wang,Ying (Wed Jun 18 2008 - 13:07:13 PDT)
- AMBER: sp carbon notation? Laura Benton (Wed Jun 18 2008 - 16:16:35 PDT)
- AMBER: questions about gaff yzhao (Wed Jun 18 2008 - 19:01:45 PDT)
- AMBER: [Fwd: failure to load box parameters] Daniel Smith (Wed Jun 18 2008 - 20:58:10 PDT)
- AMBER: How to create average structure? Shen, Lingling (Wed Jun 18 2008 - 21:44:03 PDT)
- AMBER: how to extract x,y,z of a set of atoms from an MD trajectories fatima.chami.durham.ac.uk (Thu Jun 19 2008 - 02:16:52 PDT)
- AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge) (Thu Jun 19 2008 - 03:22:53 PDT)
- AMBER: Installation Problem of AMBER10 bhargav patel (Thu Jun 19 2008 - 03:57:26 PDT)
- AMBER: How to extract solvent box information from .rst or .mdcrd files? Panwang Zhou (Thu Jun 19 2008 - 07:13:18 PDT)
- AMBER: simple sander James W. Caldwell (Thu Jun 19 2008 - 16:30:39 PDT)
- AMBER: ligand complexed simulation Siddharth Rastogi (Fri Jun 20 2008 - 00:14:18 PDT)
- AMBER: GAFF for organic crystals Rabone, Jeremy (Fri Jun 20 2008 - 01:05:18 PDT)
- AMBER: rdparm help Alan (Fri Jun 20 2008 - 04:12:17 PDT)
- AMBER: AmberTools 1.0 installation error: x86_64 Matthew Danielson (Fri Jun 20 2008 - 08:44:21 PDT)
- AMBER: Amber 10 timing Ed Pate (Fri Jun 20 2008 - 10:08:37 PDT)
- AMBER: SIZE.h problems 欧阳德方 (Sat Jun 21 2008 - 05:33:49 PDT)
- AMBER: (no subject) Daniel B. Kaplan (Sun Jun 22 2008 - 16:46:17 PDT)
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Sun Jun 22 2008 - 22:07:34 PDT)
- AMBER: How to adjust the problem of "Vlimit exceeded" Biman Jana (Mon Jun 23 2008 - 00:28:27 PDT)
- AMBER: How to confirm atom types of small molecule perceived by antechamber xiaonan zhang (Mon Jun 23 2008 - 01:39:30 PDT)
- AMBER: source of AMBER9 Germain Vallverdu (Mon Jun 23 2008 - 07:09:29 PDT)
- AMBER: amber10/dat/leap/cmd/README need update Alan (Mon Jun 23 2008 - 07:59:21 PDT)
- AMBER: Antechamber Question Daniel B. Kaplan (Mon Jun 23 2008 - 09:51:28 PDT)
- AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 18:01:33 PDT)
- AMBER: dihedral energy calculation inconsistent with gaussian's result Q733 (Mon Jun 23 2008 - 19:43:36 PDT)
- AMBER: unsubscribe amber sanket.deshmukh.ucd.ie (Tue Jun 24 2008 - 04:07:42 PDT)
- AMBER: A-prime RNA input file 欧阳德方 (Tue Jun 24 2008 - 04:16:27 PDT)
- AMBER: qmmm_DFTB problem Dr. Xiaofeng (Frank) Duan (Tue Jun 24 2008 - 06:58:46 PDT)
- AMBER: Compilation of amber8 patched with ramd Francesco Pietra (Tue Jun 24 2008 - 07:32:54 PDT)
- AMBER: dihedral potential with odd periodicity Germain Vallverdu (Tue Jun 24 2008 - 07:43:26 PDT)
- AMBER: Using AMBER forces Steven Winfield (Tue Jun 24 2008 - 08:44:41 PDT)
- AMBER: rdparm Segmentation fault on Ubuntu Alan (Tue Jun 24 2008 - 08:50:12 PDT)
- AMBER: how to derive torsional angle parameters in gaff Junmei Wang (Tue Jun 24 2008 - 18:45:42 PDT)
- AMBER: Debugf AMBER9 John Palmeri (Wed Jun 25 2008 - 00:38:53 PDT)
- AMBER: TI calculations in Amber10 Samuel Genheden (a03samge) (Wed Jun 25 2008 - 04:58:28 PDT)
- AMBER: A problem of dihedral angle Harry (Yicun) Ni (Wed Jun 25 2008 - 08:31:24 PDT)
- AMBER: amber10 compile gfortran question James W. Caldwell (Wed Jun 25 2008 - 11:10:58 PDT)
- AMBER: sleap - TER-card In Hee Park (Wed Jun 25 2008 - 12:14:39 PDT)
- AMBER: rdparm Segmentation fault Alan (Wed Jun 25 2008 - 14:24:34 PDT)
- AMBER: Antechamber/mopac am1-bcc charge Dong Xu (Wed Jun 25 2008 - 15:09:39 PDT)
- AMBER: (no subject) Daniel B. Kaplan (Wed Jun 25 2008 - 19:23:43 PDT)
- AMBER: Amber:unsubscribe amber sanket.deshmukh.ucd.ie (Thu Jun 26 2008 - 04:53:22 PDT)
- AMBER: concerning force fields Adrien Delmont (Thu Jun 26 2008 - 08:14:15 PDT)
- AMBER: Peseckis, Steven M. (Thu Jun 26 2008 - 08:54:05 PDT)
- AMBER: ligand partial charge and conformation question Dong Xu (Thu Jun 26 2008 - 11:01:31 PDT)
- AMBER: output file AMBER9_MPI Vijay Manickam Achari (Thu Jun 26 2008 - 12:06:19 PDT)
- AMBER: Dihedral Angle Parameters Ilyas Yildirim (Thu Jun 26 2008 - 14:07:16 PDT)
- AMBER: REMD Amber10 : error in reading namelist cntrl rebeca (Fri Jun 27 2008 - 02:01:26 PDT)
- AMBER: Group specification problem fatima.chami.durham.ac.uk (Fri Jun 27 2008 - 05:59:09 PDT)
- AMBER: pmemd 10 output Vlad Cojocaru (Fri Jun 27 2008 - 08:48:35 PDT)
- AMBER: Test scripts James W. Caldwell (Fri Jun 27 2008 - 09:35:26 PDT)
- AMBER: ptraj - read in part of trajectory Seth Lilavivat (Fri Jun 27 2008 - 09:41:51 PDT)
- AMBER: question about the charge Harry (Yicun) Ni (Fri Jun 27 2008 - 13:37:55 PDT)
- AMBER: Seed for random number generator Francesco Pietra (Sun Jun 29 2008 - 01:22:12 PDT)
- AMBER: Constrained group fatima.chami.durham.ac.uk (Mon Jun 30 2008 - 02:54:02 PDT)
- AMBER: NMR refinement teresa.ierano.unina.it (Mon Jun 30 2008 - 03:37:48 PDT)
- AMBER: nmode analysis Joachim Reichelt (Mon Jun 30 2008 - 04:53:21 PDT)
- AMBER: hold atoms fixed Boutheina Kerkeni (Mon Jun 30 2008 - 05:51:17 PDT)
- AMBER: wrapping a restart file fatima.chami.durham.ac.uk (Mon Jun 30 2008 - 07:40:58 PDT)
- AMBER: watershell cero? rebeca (Mon Jun 30 2008 - 09:22:11 PDT)
- AMBER: (no subject) fatima.chami.durham.ac.uk (Mon Jun 30 2008 - 09:26:23 PDT)
- AMBER: MM-PBSA calculation problem Wei Huang (Mon Jun 30 2008 - 09:41:16 PDT)
- AMBER: error in reading namelist cntrl Maria Frushicheva (Mon Jun 30 2008 - 13:02:50 PDT)
- AMBER: Regarding force field ff02 and ion library Abhishek Singh (Mon Jun 30 2008 - 13:54:52 PDT)
- AMBER: missing torsion parameters John Bennett (Mon Jun 30 2008 - 14:06:07 PDT)
- Last message date: Wed Jul 02 2008 - 06:07:29 PDT
- Archived on: Mon Dec 23 2024 - 05:53:37 PST
