Amber Archive Oct 2006 by thread
- Re: AMBER: chemical shift restrains David A. Case (Sun Oct 01 2006 - 06:35:01 PDT)
- Re: AMBER: RE: Amber8: problem related to antechamber David A. Case (Sun Oct 01 2006 - 06:35:55 PDT)
- Re: AMBER: Multiple Timestep MD David A. Case (Sun Oct 01 2006 - 06:35:25 PDT)
- Re: AMBER: RE: Amber8: problem related to antechamber David A. Case (Sun Oct 01 2006 - 06:34:45 PDT)
- AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth (Sun Oct 01 2006 - 19:15:54 PDT)
- Re: AMBER: proposed patch for ptraj/evec.c (Amber 9.0) David A. Case (Mon Oct 02 2006 - 08:51:53 PDT)
- Re: AMBER: problem to center solvateshell David A. Case (Mon Oct 02 2006 - 09:01:44 PDT)
- AMBER: how to run a mm_pbsa on a minimized structure? Wang, Xuelin (Mon Oct 02 2006 - 14:50:02 PDT)
- Re: AMBER: mdcrd file Bill Ross (Mon Oct 02 2006 - 17:23:18 PDT)
- AMBER: How to get the VDW contacts' messages from the mdcrd files Jiapu.Zhang.csiro.au (Mon Oct 02 2006 - 23:11:03 PDT)
- RE: AMBER: problem to center solvateshell Bonnet, Pascal [PRDBE] (Mon Oct 02 2006 - 23:30:53 PDT)
- AMBER: Pressure problem with restraint Jianhui (Tue Oct 03 2006 - 07:41:46 PDT)
- AMBER: hbond analysis Vlad Cojocaru (Tue Oct 03 2006 - 08:45:23 PDT)
- AMBER: MM_PBSA error Shozeb Haider (Tue Oct 03 2006 - 14:04:57 PDT)
- AMBER: how to calculate rmsd for non hydrogen at oms? yxiong99 (Tue Oct 03 2006 - 09:43:49 PDT)
- AMBER: Re: Distance between two atoms Fenghui Fan (Tue Oct 03 2006 - 23:12:06 PDT)
- AMBER: Re: atom nomination in the PDB file produced by Amber Fenghui Fan (Wed Oct 04 2006 - 08:41:11 PDT)
- AMBER: change from .rst file to .mdcrd file Wang, Xuelin (Wed Oct 04 2006 - 08:52:56 PDT)
- Re: AMBER: on rst file Bill Ross (Wed Oct 04 2006 - 10:17:10 PDT)
- AMBER: Is GB/SANDER slower than TIP3P/PMEMD b86203054.ntu.edu.tw (Wed Oct 04 2006 - 10:21:39 PDT)
- AMBER: AMBER minimization vs. Gaussian optimization Ilyas Yildirim (Wed Oct 04 2006 - 13:27:48 PDT)
- AMBER: ptraj hbond analysis troubles Sayandeep Purkayasth (Wed Oct 04 2006 - 14:14:10 PDT)
- AMBER: VMD PDB into LEAP Readable PDB Akshay Patny (Wed Oct 04 2006 - 18:07:11 PDT)
- AMBER: Missing values for MM VDW bala (Thu Oct 05 2006 - 04:33:14 PDT)
- AMBER: PBSA calculation fail .... Changge Ji (Thu Oct 05 2006 - 06:42:39 PDT)
- AMBER: generating resp input files with antechamber dhruva chakravorty (Thu Oct 05 2006 - 12:53:03 PDT)
- AMBER: water prmtop/inpcrd problem Akshay Patny (Thu Oct 05 2006 - 18:08:59 PDT)
- Re: Re: AMBER: PBSA calculation fail .... Changge Ji (Thu Oct 05 2006 - 19:36:34 PDT)
- AMBER: (no subject) Prashanth Athri (Thu Oct 05 2006 - 19:34:47 PDT)
- AMBER: Calculation of Dihedral constants Prashanth Athri (Thu Oct 05 2006 - 19:36:15 PDT)
- AMBER: LEAP error Akshay Patny (Fri Oct 06 2006 - 09:49:42 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Fri Oct 06 2006 - 10:13:15 PDT)
- AMBER: How to merge two molecules to one Myunggi Yi (Fri Oct 06 2006 - 11:51:19 PDT)
- AMBER: MM_PBSA Rajendra P. OJHA (Sat Oct 07 2006 - 09:21:49 PDT)
- AMBER: question about building molecules Rita Cassia (Sun Oct 08 2006 - 04:05:59 PDT)
- AMBER: some puzzles in equilibration MD Zhihong Yu (Mon Oct 09 2006 - 06:58:06 PDT)
- AMBER: Trouble with Leap Biswa Ranjan Meher (Mon Oct 09 2006 - 07:28:28 PDT)
- AMBER: MMPBSA vDW error Shozeb Haider (Mon Oct 09 2006 - 16:08:27 PDT)
- AMBER: Announcement: Parameters for Modified Nucleosides in RNA Raviprasad Aduri (Mon Oct 09 2006 - 14:13:56 PDT)
- AMBER: partial charges Fabian Alejandro Rodriguez (Tue Oct 10 2006 - 09:35:53 PDT)
- AMBER: generalized born model for organic solvent Eric Hu (Tue Oct 10 2006 - 18:29:12 PDT)
- AMBER: adding polar hydrogens Sean Rathlef (Tue Oct 10 2006 - 19:43:39 PDT)
- AMBER: Reducind trajectory Sergey Samsonov (Wed Oct 11 2006 - 00:03:49 PDT)
- AMBER: amber force field Noriaki Okimoto (Wed Oct 11 2006 - 11:21:03 PDT)
- AMBER: problems for running sander.MPI Qizhi Cui (Wed Oct 11 2006 - 13:39:36 PDT)
- AMBER: puzzles about solvatoct or solvatebox Zhihong Yu (Thu Oct 12 2006 - 03:00:08 PDT)
- AMBER: High Values in MMPBSA Shozeb Haider (Thu Oct 12 2006 - 09:55:15 PDT)
- AMBER: angle between two vectors Lwin, ThuZar (Thu Oct 12 2006 - 09:51:15 PDT)
- Re: AMBER: puzzles about solvatoct or solvatebox Bill Ross (Thu Oct 12 2006 - 10:43:38 PDT)
- AMBER: Phenyl Ring atom types sethl.gatech.edu (Thu Oct 12 2006 - 11:59:24 PDT)
- AMBER: Ptraj problems Charlisa Daniels (Thu Oct 12 2006 - 13:01:30 PDT)
- AMBER: TFE parameters for Amber Mingfeng Yang (Thu Oct 12 2006 - 16:33:21 PDT)
- AMBER: BioBlade Sean Rathlef (Thu Oct 12 2006 - 20:12:41 PDT)
- AMBER: klambda Sergey Samsonov (Fri Oct 13 2006 - 07:49:05 PDT)
- AMBER: Updated Tutorials Page Ross Walker (Fri Oct 13 2006 - 12:17:07 PDT)
- AMBER: force fiels for a-rna asli ertekin (Fri Oct 13 2006 - 15:28:58 PDT)
- Re: AMBER: restraints and constant pressure Joshua (Fri Oct 13 2006 - 15:46:26 PDT)
- AMBER: SURFTEN/SURFOFF values in amber9 ferranna.unimo.it (Sat Oct 14 2006 - 00:27:42 PDT)
- AMBER: Grid command of ptraj Atsutoshi Okabe (Sat Oct 14 2006 - 00:31:01 PDT)
- AMBER: How to calculate RDF based on the center of mass of specific solute atoms? Xioling Chuang (Sun Oct 15 2006 - 21:04:10 PDT)
- AMBER: simulation of protein in non-aq or organic solvent bath Smriti Sharma (Sun Oct 15 2006 - 21:06:53 PDT)
- AMBER: Amber8: problem related to antechamber priya priya (Mon Oct 16 2006 - 00:00:38 PDT)
- AMBER: Amber8: how to do Simulated Annealing and Equilibration priya priya (Mon Oct 16 2006 - 01:32:18 PDT)
- AMBER: modeling of ligand concentrations Sean Rathlef (Mon Oct 16 2006 - 13:43:51 PDT)
- AMBER: Density calculation Jianhui (Mon Oct 16 2006 - 14:12:24 PDT)
- RE: AMBER: angle between two vectors. . Lwin, ThuZar (Mon Oct 16 2006 - 13:51:28 PDT)
- AMBER: How to find equillibration time for my system in a generalised born solvation model Gobind Singh Bisht (Mon Oct 16 2006 - 14:34:11 PDT)
- AMBER: regarding PBCAL in MM-PBSA Cenk Andac (Mon Oct 16 2006 - 16:11:33 PDT)
- AMBER: General Coding Problem Elijah Gregory (Mon Oct 16 2006 - 16:53:27 PDT)
- Re: AMBER: General Coding Problem Bill Ross (Mon Oct 16 2006 - 17:56:37 PDT)
- AMBER: Problem working with Antechamber nur avneet (Tue Oct 17 2006 - 00:44:54 PDT)
- AMBER: RDF calculation Xioling Chuang (Tue Oct 17 2006 - 03:54:02 PDT)
- AMBER: How did the coordinates change in xleap? Zhihong Yu (Tue Oct 17 2006 - 08:03:47 PDT)
- AMBER: Unstable RMS trajectory Dave, Sonya (Tue Oct 17 2006 - 09:03:59 PDT)
- AMBER: sander/topology problem Lorenzo Gontrani (Tue Oct 17 2006 - 09:51:39 PDT)
- AMBER: question on mm_pbsa_statistics.pl Yongmei Pan (Tue Oct 17 2006 - 15:36:23 PDT)
- AMBER: questions on mm_pbsa_statitistics.pl Yongmei Pan (Tue Oct 17 2006 - 15:57:59 PDT)
- AMBER: Problem loading peptoid residues with antechamber nur avneet (Tue Oct 17 2006 - 23:23:42 PDT)
- AMBER: To create methanol solvent box Atsutoshi Okabe (Tue Oct 17 2006 - 23:31:02 PDT)
- AMBER: how to simulate water flow inside a channel? Gobind Singh Bisht (Wed Oct 18 2006 - 07:33:51 PDT)
- AMBER: alanine scan (mm/pbsa) rob yang (Wed Oct 18 2006 - 07:46:47 PDT)
- Re: Re: AMBER: questions on mm_pbsa_statitistics.pl Yongmei Pan (Wed Oct 18 2006 - 08:12:58 PDT)
- AMBER: ptraj atomicfluct Myunggi Yi (Wed Oct 18 2006 - 11:59:22 PDT)
- AMBER: charge models in antechamber Eric Hu (Wed Oct 18 2006 - 15:51:00 PDT)
- AMBER: RESP charges of iron-porphyrin system Shin Tokumoto (Wed Oct 18 2006 - 19:50:26 PDT)
- AMBER: mmpbsa in parallell Olayiwola Adekoya (Thu Oct 19 2006 - 00:57:07 PDT)
- AMBER: Free-energy using MM-PBSA mathew k varghese (Thu Oct 19 2006 - 01:05:45 PDT)
- AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Maniopoulou, A \(Mina\) (Thu Oct 19 2006 - 05:48:08 PDT)
- AMBER: Amber 9 installation problem Cenk Andac (Thu Oct 19 2006 - 08:43:02 PDT)
- AMBER: Curve fitting during dihedral parameter calculation Prashanth Athri (Thu Oct 19 2006 - 12:15:21 PDT)
- AMBER: Issue with installation of Amber v9.0 parallel compilation Pravin_Kumar.jubilantbiosys.com (Thu Oct 19 2006 - 21:02:42 PDT)
- AMBER: Issue with installation of Amber v9.0 parallel compilation Pravin_Kumar.jubilantbiosys.com (Thu Oct 19 2006 - 21:17:51 PDT)
- AMBER: Probelm with running Amber 9 parallelly Rafi Ahmad (Fri Oct 20 2006 - 07:29:14 PDT)
- AMBER: rbornstat average and fluctuations incorrect when nrespa != nrespai Ingvar Lagerstedt (Fri Oct 20 2006 - 09:17:08 PDT)
- AMBER: Question about sander code Kijeong Kwac (Fri Oct 20 2006 - 11:13:49 PDT)
- AMBER: problem of installing carnal on macosx gtg549i.mail.gatech.edu (Fri Oct 20 2006 - 11:37:39 PDT)
- Re: AMBER: problem of installing carnal on macosx Bill Ross (Fri Oct 20 2006 - 11:50:19 PDT)
- AMBER: atom type nh vs. n2 sethl.gatech.edu (Fri Oct 20 2006 - 14:31:09 PDT)
- AMBER: question on molsurf Yongmei Pan (Fri Oct 20 2006 - 15:38:38 PDT)
- AMBER: HBON in frcmod file Ilyas Yildirim (Fri Oct 20 2006 - 22:46:31 PDT)
- Re: AMBER: HBON in frcmod file Bill Ross (Sat Oct 21 2006 - 00:41:55 PDT)
- AMBER: single or dual topology for TI? Holly Freedman (Sat Oct 21 2006 - 11:20:51 PDT)
- AMBER: mmpbsa: fail to run heat in tutorial A3 jitrayut jitonnom (Sun Oct 22 2006 - 10:31:53 PDT)
- AMBER: Virus? Peter Gannett (Mon Oct 23 2006 - 05:34:29 PDT)
- AMBER: ff for drug-dna complex and drug atom types assignment Kateryna Miroshnychenko (Mon Oct 23 2006 - 09:08:59 PDT)
- AMBER: Using modified NA bases sethl.gatech.edu (Mon Oct 23 2006 - 12:59:15 PDT)
- AMBER: ptraj radial problem: Segmentation fault Jianhui Tian (Mon Oct 23 2006 - 14:48:43 PDT)
- AMBER: splitting LES with ptraj in amber9 bala (Mon Oct 23 2006 - 22:18:16 PDT)
- AMBER: DIST_RST Urszula Uciechowska (Tue Oct 24 2006 - 01:32:03 PDT)
- AMBER: problem with calcpka.pl Benjamin Juhl (Tue Oct 24 2006 - 04:58:27 PDT)
- AMBER: pmemd installation on linux_p3_athlon ifort gtg549i.mail.gatech.edu (Tue Oct 24 2006 - 09:20:30 PDT)
- AMBER: load charges to antechamber calculations Wang, Xuelin (Tue Oct 24 2006 - 12:30:24 PDT)
- AMBER: md and implicit solvation Jardas sucuriba (Tue Oct 24 2006 - 16:57:24 PDT)
- AMBER: error estimate for free energy perturbation calculation jz7.duke.edu (Tue Oct 24 2006 - 21:15:26 PDT)
- AMBER: Question regarding lastrst and taup Priti Hansia (Tue Oct 24 2006 - 23:37:09 PDT)
- AMBER: parameters !!?? Urszula Uciechowska (Wed Oct 25 2006 - 02:27:22 PDT)
- AMBER: Shake&Lone Pairs Lorenzo Gontrani (Wed Oct 25 2006 - 03:58:59 PDT)
- AMBER: amber9: SA Bomb in sa_arc Giulio Rastelli (Wed Oct 25 2006 - 04:03:54 PDT)
- AMBER: residence time& hydration density Andres Palencia (Wed Oct 25 2006 - 07:16:53 PDT)
- AMBER: reinstall amber8 Rachel (Wed Oct 25 2006 - 07:57:59 PDT)
- AMBER: mm_pbsa: binding energy calculation Varsha Goyal (Wed Oct 25 2006 - 11:51:57 PDT)
- AMBER: how to select the problematic residues(atoms) in VMD Rachel (Thu Oct 26 2006 - 04:00:21 PDT)
- AMBER: MM-PBSA memory usage Stefano Pieraccini (Thu Oct 26 2006 - 05:33:41 PDT)
- AMBER: Calculating native contacts for mdcrd files Anna Bowman (Thu Oct 26 2006 - 08:20:50 PDT)
- AMBER: how to add hydrogen molecules in the protein Rachel (Thu Oct 26 2006 - 09:28:16 PDT)
- AMBER: error GRID command in ptraj Andres Palencia (Thu Oct 26 2006 - 10:39:19 PDT)
- AMBER: parameters for fluoromolecules with more than one single carbon? Jones de Andrade (Thu Oct 26 2006 - 14:51:27 PDT)
- AMBER: halogen bondi radii in mm_pbsa_calceneent.pm Giulio Rastelli (Fri Oct 27 2006 - 01:46:30 PDT)
- AMBER: Compile AMBER 8 Esther Brugger (Fri Oct 27 2006 - 08:44:51 PDT)
- AMBER: where to set bondi radii for halogens Giulio Rastelli (Fri Oct 27 2006 - 09:59:00 PDT)
- AMBER: Amber: Parallel Installation Problems Maniopoulou, A \(Mina\) (Fri Oct 27 2006 - 10:13:56 PDT)
- AMBER: Help with polarization force field norberto.ualberta.ca (Fri Oct 27 2006 - 16:20:09 PDT)
- AMBER: RESP charge fitting Mingfeng Yang (Fri Oct 27 2006 - 17:35:37 PDT)
- AMBER: solvation and His protonation Jardas sucuriba (Sat Oct 28 2006 - 07:00:44 PDT)
- AMBER: ff02 force fields norberto.ualberta.ca (Sun Oct 29 2006 - 12:18:25 PST)
- AMBER: C -N -CT-CT torsion parameters John Vieceli (Sun Oct 29 2006 - 17:10:49 PST)
- AMBER: Closest(closest water) Sergey Samsonov (Mon Oct 30 2006 - 04:58:11 PST)
- AMBER: how to restrain some residues in a NPT MD? Zhihong Yu (Mon Oct 30 2006 - 07:20:38 PST)
- AMBER: ff99SB vs ff02 (ff02pol.rl) Nicolas Lux Fawzi (Mon Oct 30 2006 - 17:48:32 PST)
- AMBER: Re: Problems installing antechamber 1.27 andrea carotti (Tue Oct 31 2006 - 00:17:49 PST)
- AMBER: what is the RMS value in resp charge fitting ? jitrayut jitonnom (Tue Oct 31 2006 - 00:46:31 PST)
- AMBER: MMPBSA entropy question Barbault Florent (Tue Oct 31 2006 - 01:08:55 PST)
- AMBER: Problems with carnal (Amber7) anna.schrey.gmx.de (Tue Oct 31 2006 - 07:24:29 PST)
- Re: AMBER: Problems with carnal (Amber7) Bill Ross (Tue Oct 31 2006 - 09:09:57 PST)
- AMBER: N1-protonated adenosine, N-terminal myristyl group Michael F. Summers (Tue Oct 31 2006 - 12:54:49 PST)
- AMBER: mm_pbsa does not terminate Holly Freedman (Tue Oct 31 2006 - 16:51:19 PST)
- Last message date: Sun Nov 05 2006 - 06:07:31 PST
- Archived on: Fri Dec 20 2024 - 05:53:34 PST
