AMBER Archive (2006) - Oct 2006 By ThreadMost recent messages
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Starting: Sun Oct 01 2006 - 08:34:45 CDT
Ending: Tue Oct 31 2006 - 19:04:29 CST
- AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth (Sun Oct 01 2006 - 21:15:54 CDT)
- AMBER: how to run a mm_pbsa on a minimized structure? Wang, Xuelin (Mon Oct 02 2006 - 16:50:02 CDT)
- Re: AMBER: mdcrd file Bill Ross (Mon Oct 02 2006 - 19:23:18 CDT)
- AMBER: How to get the VDW contacts' messages from the mdcrd files Jiapu.Zhang_at_csiro.au (Tue Oct 03 2006 - 01:11:03 CDT)
- AMBER: Pressure problem with restraint Jianhui (Tue Oct 03 2006 - 09:41:46 CDT)
- AMBER: hbond analysis Vlad Cojocaru (Tue Oct 03 2006 - 10:45:23 CDT)
- AMBER: MM_PBSA error Shozeb Haider (Tue Oct 03 2006 - 16:04:57 CDT)
- AMBER: how to calculate rmsd for non hydrogen at oms? yxiong99 (Tue Oct 03 2006 - 11:43:49 CDT)
- AMBER: Re: Distance between two atoms Fenghui Fan (Wed Oct 04 2006 - 01:12:06 CDT)
- AMBER: Re: atom nomination in the PDB file produced by Amber Fenghui Fan (Wed Oct 04 2006 - 10:41:11 CDT)
- AMBER: change from .rst file to .mdcrd file Wang, Xuelin (Wed Oct 04 2006 - 10:52:56 CDT)
- Re: AMBER: on rst file Bill Ross (Wed Oct 04 2006 - 12:17:10 CDT)
- Re: AMBER: Is GB/SANDER slower than TIP3P/PMEMD Robert Duke (Wed Oct 04 2006 - 12:45:06 CDT)
- AMBER: AMBER minimization vs. Gaussian optimization Ilyas Yildirim (Wed Oct 04 2006 - 15:27:48 CDT)
- AMBER: ptraj hbond analysis troubles Sayandeep Purkayasth (Wed Oct 04 2006 - 16:14:10 CDT)
- AMBER: VMD PDB into LEAP Readable PDB Akshay Patny (Wed Oct 04 2006 - 20:07:11 CDT)
- AMBER: Missing values for MM VDW bala (Thu Oct 05 2006 - 06:33:14 CDT)
- AMBER: PBSA calculation fail .... Changge Ji (Thu Oct 05 2006 - 08:42:39 CDT)
- AMBER: generating resp input files with antechamber dhruva chakravorty (Thu Oct 05 2006 - 14:53:03 CDT)
- AMBER: water prmtop/inpcrd problem Akshay Patny (Thu Oct 05 2006 - 20:08:59 CDT)
- AMBER: Calculation of Dihedral constants Prashanth Athri (Thu Oct 05 2006 - 21:36:15 CDT)
- AMBER: (no subject) Prashanth Athri (Thu Oct 05 2006 - 21:34:47 CDT)
- AMBER: LEAP error Akshay Patny (Fri Oct 06 2006 - 11:49:42 CDT)
- AMBER: How to merge two molecules to one Myunggi Yi (Fri Oct 06 2006 - 13:51:19 CDT)
- AMBER: MM_PBSA Rajendra P. OJHA (Sat Oct 07 2006 - 11:21:49 CDT)
- AMBER: question about building molecules Rita Cassia (Sun Oct 08 2006 - 06:05:59 CDT)
- AMBER: some puzzles in equilibration MD Zhihong Yu (Mon Oct 09 2006 - 08:58:06 CDT)
- AMBER: Trouble with Leap Biswa Ranjan Meher (Mon Oct 09 2006 - 09:28:28 CDT)
- AMBER: MMPBSA vDW error Shozeb Haider (Mon Oct 09 2006 - 18:08:27 CDT)
- AMBER: Announcement: Parameters for Modified Nucleosides in RNA Raviprasad Aduri (Mon Oct 09 2006 - 16:13:56 CDT)
- AMBER: partial charges Fabian Alejandro Rodriguez (Tue Oct 10 2006 - 11:35:53 CDT)
- AMBER: generalized born model for organic solvent Eric Hu (Tue Oct 10 2006 - 20:29:12 CDT)
- AMBER: adding polar hydrogens Sean Rathlef (Tue Oct 10 2006 - 21:43:39 CDT)
- AMBER: Reducind trajectory Sergey Samsonov (Wed Oct 11 2006 - 02:03:49 CDT)
- AMBER: amber force field Noriaki Okimoto (Wed Oct 11 2006 - 13:21:03 CDT)
- AMBER: problems for running sander.MPI Qizhi Cui (Wed Oct 11 2006 - 15:39:36 CDT)
- AMBER: puzzles about solvatoct or solvatebox Zhihong Yu (Thu Oct 12 2006 - 05:00:08 CDT)
- AMBER: High Values in MMPBSA Shozeb Haider (Thu Oct 12 2006 - 11:55:15 CDT)
- AMBER: angle between two vectors Lwin, ThuZar (Thu Oct 12 2006 - 11:51:15 CDT)
- Re: AMBER: puzzles about solvatoct or solvatebox Bill Ross (Thu Oct 12 2006 - 12:43:38 CDT)
- AMBER: Phenyl Ring atom types sethl_at_gatech.edu (Thu Oct 12 2006 - 13:59:24 CDT)
- AMBER: Ptraj problems Charlisa Daniels (Thu Oct 12 2006 - 15:01:30 CDT)
- AMBER: TFE parameters for Amber Mingfeng Yang (Thu Oct 12 2006 - 18:33:21 CDT)
- AMBER: klambda Sergey Samsonov (Fri Oct 13 2006 - 09:49:05 CDT)
- AMBER: Updated Tutorials Page Ross Walker (Fri Oct 13 2006 - 14:17:07 CDT)
- AMBER: force fiels for a-rna asli ertekin (Fri Oct 13 2006 - 17:28:58 CDT)
- AMBER: Grid command of ptraj Atsutoshi Okabe (Sat Oct 14 2006 - 02:31:01 CDT)
- AMBER: SURFTEN/SURFOFF values in amber9 ferranna_at_unimo.it (Sat Oct 14 2006 - 02:27:42 CDT)
- AMBER: How to calculate RDF based on the center of mass of specific solute atoms? Xioling Chuang (Sun Oct 15 2006 - 23:04:10 CDT)
- AMBER: simulation of protein in non-aq or organic solvent bath Smriti Sharma (Sun Oct 15 2006 - 23:06:53 CDT)
- AMBER: Amber8: problem related to antechamber priya priya (Mon Oct 16 2006 - 02:00:38 CDT)
- AMBER: Amber8: how to do Simulated Annealing and Equilibration priya priya (Mon Oct 16 2006 - 03:32:18 CDT)
- RE: AMBER: angle between two vectors. . Lwin, ThuZar (Mon Oct 16 2006 - 15:51:28 CDT)
- AMBER: modeling of ligand concentrations Sean Rathlef (Mon Oct 16 2006 - 15:43:51 CDT)
- AMBER: Density calculation Jianhui (Mon Oct 16 2006 - 16:12:24 CDT)
- AMBER: How to find equillibration time for my system in a generalised born solvation model Gobind Singh Bisht (Mon Oct 16 2006 - 16:34:11 CDT)
- AMBER: regarding PBCAL in MM-PBSA Cenk Andac (Mon Oct 16 2006 - 18:11:33 CDT)
- AMBER: General Coding Problem Elijah Gregory (Mon Oct 16 2006 - 18:53:27 CDT)
- Re: AMBER: General Coding Problem Bill Ross (Mon Oct 16 2006 - 19:56:37 CDT)
- AMBER: Problem working with Antechamber nur avneet (Tue Oct 17 2006 - 02:44:54 CDT)
- AMBER: RDF calculation Xioling Chuang (Tue Oct 17 2006 - 05:54:02 CDT)
- AMBER: How did the coordinates change in xleap? Zhihong Yu (Tue Oct 17 2006 - 10:03:47 CDT)
- AMBER: Unstable RMS trajectory Dave, Sonya (Tue Oct 17 2006 - 11:03:59 CDT)
- AMBER: sander/topology problem Lorenzo Gontrani (Tue Oct 17 2006 - 11:51:39 CDT)
- AMBER: question on mm_pbsa_statistics.pl Yongmei Pan (Tue Oct 17 2006 - 17:36:23 CDT)
- AMBER: questions on mm_pbsa_statitistics.pl Yongmei Pan (Tue Oct 17 2006 - 17:57:59 CDT)
- AMBER: Problem loading peptoid residues with antechamber nur avneet (Wed Oct 18 2006 - 01:23:42 CDT)
- AMBER: To create methanol solvent box Atsutoshi Okabe (Wed Oct 18 2006 - 01:31:02 CDT)
- AMBER: how to simulate water flow inside a channel? Gobind Singh Bisht (Wed Oct 18 2006 - 09:33:51 CDT)
- AMBER: alanine scan (mm/pbsa) rob yang (Wed Oct 18 2006 - 09:46:47 CDT)
- AMBER: ptraj atomicfluct Myunggi Yi (Wed Oct 18 2006 - 13:59:22 CDT)
- AMBER: charge models in antechamber Eric Hu (Wed Oct 18 2006 - 17:51:00 CDT)
- AMBER: RESP charges of iron-porphyrin system Shin Tokumoto (Wed Oct 18 2006 - 21:50:26 CDT)
- AMBER: mmpbsa in parallell Olayiwola Adekoya (Thu Oct 19 2006 - 02:57:07 CDT)
- AMBER: Free-energy using MM-PBSA mathew k varghese (Thu Oct 19 2006 - 03:05:45 CDT)
- AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Maniopoulou, A \(Mina\) (Thu Oct 19 2006 - 07:48:08 CDT)
- AMBER: Curve fitting during dihedral parameter calculation Prashanth Athri (Thu Oct 19 2006 - 14:15:21 CDT)
- AMBER: Issue with installation of Amber v9.0 parallel compilation Pravin_Kumar_at_jubilantbiosys.com (Thu Oct 19 2006 - 23:02:42 CDT)
- AMBER: Issue with installation of Amber v9.0 parallel compilation Pravin_Kumar_at_jubilantbiosys.com (Thu Oct 19 2006 - 23:17:51 CDT)
- AMBER: Probelm with running Amber 9 parallelly Rafi Ahmad (Fri Oct 20 2006 - 09:29:14 CDT)
- AMBER: rbornstat average and fluctuations incorrect when nrespa != nrespai Ingvar Lagerstedt (Fri Oct 20 2006 - 11:17:08 CDT)
- AMBER: Question about sander code Kijeong Kwac (Fri Oct 20 2006 - 13:13:49 CDT)
- AMBER: problem of installing carnal on macosx gtg549i_at_mail.gatech.edu (Fri Oct 20 2006 - 13:37:39 CDT)
- Re: AMBER: problem of installing carnal on macosx Bill Ross (Fri Oct 20 2006 - 13:50:19 CDT)
- AMBER: atom type nh vs. n2 sethl_at_gatech.edu (Fri Oct 20 2006 - 16:31:09 CDT)
- AMBER: question on molsurf Yongmei Pan (Fri Oct 20 2006 - 17:38:38 CDT)
- AMBER: HBON in frcmod file Ilyas Yildirim (Sat Oct 21 2006 - 00:46:31 CDT)
- Re: AMBER: HBON in frcmod file Bill Ross (Sat Oct 21 2006 - 02:41:55 CDT)
- AMBER: single or dual topology for TI? Holly Freedman (Sat Oct 21 2006 - 13:20:51 CDT)
- AMBER: mmpbsa: fail to run heat in tutorial A3 jitrayut jitonnom (Sun Oct 22 2006 - 12:31:53 CDT)
- AMBER: Virus? Peter Gannett (Mon Oct 23 2006 - 07:34:29 CDT)
- AMBER: ff for drug-dna complex and drug atom types assignment Kateryna Miroshnychenko (Mon Oct 23 2006 - 11:08:59 CDT)
- AMBER: Using modified NA bases sethl_at_gatech.edu (Mon Oct 23 2006 - 14:59:15 CDT)
- AMBER: ptraj radial problem: Segmentation fault Jianhui Tian (Mon Oct 23 2006 - 16:48:43 CDT)
- AMBER: splitting LES with ptraj in amber9 bala (Tue Oct 24 2006 - 00:18:16 CDT)
- AMBER: DIST_RST Urszula Uciechowska (Tue Oct 24 2006 - 03:32:03 CDT)
- AMBER: problem with calcpka.pl Benjamin Juhl (Tue Oct 24 2006 - 06:58:27 CDT)
- AMBER: pmemd installation on linux_p3_athlon ifort gtg549i_at_mail.gatech.edu (Tue Oct 24 2006 - 11:20:30 CDT)
- AMBER: load charges to antechamber calculations Wang, Xuelin (Tue Oct 24 2006 - 14:30:24 CDT)
- AMBER: md and implicit solvation Jardas sucuriba (Tue Oct 24 2006 - 18:57:24 CDT)
- AMBER: error estimate for free energy perturbation calculation jz7_at_duke.edu (Tue Oct 24 2006 - 23:15:26 CDT)
- AMBER: Question regarding lastrst and taup Priti Hansia (Wed Oct 25 2006 - 01:37:09 CDT)
- AMBER: parameters !!?? Urszula Uciechowska (Wed Oct 25 2006 - 04:27:22 CDT)
- AMBER: Shake&Lone Pairs Lorenzo Gontrani (Wed Oct 25 2006 - 05:58:59 CDT)
- AMBER: amber9: SA Bomb in sa_arc Giulio Rastelli (Wed Oct 25 2006 - 06:03:54 CDT)
- AMBER: residence time& hydration density Andres Palencia (Wed Oct 25 2006 - 09:16:53 CDT)
- AMBER: reinstall amber8 Rachel (Wed Oct 25 2006 - 09:57:59 CDT)
- AMBER: mm_pbsa: binding energy calculation Varsha Goyal (Wed Oct 25 2006 - 13:51:57 CDT)
- AMBER: how to select the problematic residues(atoms) in VMD Rachel (Thu Oct 26 2006 - 06:00:21 CDT)
- AMBER: MM-PBSA memory usage Stefano Pieraccini (Thu Oct 26 2006 - 07:33:41 CDT)
- AMBER: Calculating native contacts for mdcrd files Anna Bowman (Thu Oct 26 2006 - 10:20:50 CDT)
- AMBER: how to add hydrogen molecules in the protein Rachel (Thu Oct 26 2006 - 11:28:16 CDT)
- AMBER: error GRID command in ptraj Andres Palencia (Thu Oct 26 2006 - 12:39:19 CDT)
- AMBER: parameters for fluoromolecules with more than one single carbon? Jones de Andrade (Thu Oct 26 2006 - 16:51:27 CDT)
- AMBER: halogen bondi radii in mm_pbsa_calceneent.pm Giulio Rastelli (Fri Oct 27 2006 - 03:46:30 CDT)
- AMBER: Compile AMBER 8 Esther Brugger (Fri Oct 27 2006 - 10:44:51 CDT)
- AMBER: where to set bondi radii for halogens Giulio Rastelli (Fri Oct 27 2006 - 11:59:00 CDT)
- AMBER: Amber: Parallel Installation Problems Maniopoulou, A \(Mina\) (Fri Oct 27 2006 - 12:13:56 CDT)
- AMBER: Help with polarization force field norberto_at_ualberta.ca (Fri Oct 27 2006 - 18:20:09 CDT)
- AMBER: RESP charge fitting Mingfeng Yang (Fri Oct 27 2006 - 19:35:37 CDT)
- AMBER: solvation and His protonation Jardas sucuriba (Sat Oct 28 2006 - 09:00:44 CDT)
- AMBER: ff02 force fields norberto_at_ualberta.ca (Sun Oct 29 2006 - 14:18:25 CST)
- AMBER: C -N -CT-CT torsion parameters John Vieceli (Sun Oct 29 2006 - 19:10:49 CST)
- AMBER: Closest(closest water) Sergey Samsonov (Mon Oct 30 2006 - 06:58:11 CST)
- AMBER: how to restrain some residues in a NPT MD? Zhihong Yu (Mon Oct 30 2006 - 09:20:38 CST)
- AMBER: ff99SB vs ff02 (ff02pol.rl) Nicolas Lux Fawzi (Mon Oct 30 2006 - 19:48:32 CST)
- AMBER: Re: Problems installing antechamber 1.27 andrea carotti (Tue Oct 31 2006 - 02:17:49 CST)
- AMBER: what is the RMS value in resp charge fitting ? jitrayut jitonnom (Tue Oct 31 2006 - 02:46:31 CST)
- AMBER: MMPBSA entropy question Barbault Florent (Tue Oct 31 2006 - 03:08:55 CST)
- AMBER: Problems with carnal (Amber7) anna.schrey_at_gmx.de (Tue Oct 31 2006 - 09:24:29 CST)
- Re: AMBER: Problems with carnal (Amber7) Bill Ross (Tue Oct 31 2006 - 11:09:57 CST)
- AMBER: N1-protonated adenosine, N-terminal myristyl group Michael F. Summers (Tue Oct 31 2006 - 14:54:49 CST)
- AMBER: mm_pbsa does not terminate Holly Freedman (Tue Oct 31 2006 - 18:51:19 CST)
Last message date: Sat Dec 30 2006 - 07:20:23 CST
Archived on: Wed Feb 21 2007 - 22:44:16 CST
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