Amber Archive May 2005 By Thread
- AMBER: Identifying water molecules with ptraj Joseph Fernandez (Sun May 01 2005 - 14:00:59 PDT)
- AMBER: fast 1/r methods Brent Krueger (Mon May 02 2005 - 04:51:56 PDT)
- Re: AMBER: ipol=1 & use_pme= ?? David A. Case (Mon May 02 2005 - 09:44:47 PDT)
- AMBER: How to fix the atom in NPT case? george Chen (Mon May 02 2005 - 11:19:54 PDT)
- Re: AMBER: Re: R.E.D. question Yanze Zhang (Mon May 02 2005 - 12:19:14 PDT)
- AMBER: sander run YoungJin Cho (Mon May 02 2005 - 13:45:01 PDT)
- AMBER: GB with dipoles ! Pradipta Bandyopadhyay (Tue May 03 2005 - 04:54:44 PDT)
- Fwd: Re: AMBER: AMBER Test Anthony Cruz (Tue May 03 2005 - 05:25:46 PDT)
- AMBER: Can I add iodide anione? Myunggi Yi (Tue May 03 2005 - 10:36:07 PDT)
- AMBER: rborn(i) in egb.f Harianto Tjong (Tue May 03 2005 - 12:04:39 PDT)
- AMBER: NOE constraints Hui-Hsu Tsai (Tue May 03 2005 - 12:18:27 PDT)
- AMBER: Relative stability with MMPBSA Angelo Pugliese (Wed May 04 2005 - 09:09:27 PDT)
- AMBER: Bromelain PDF xleap load error Thomas Patko (Wed May 04 2005 - 10:13:35 PDT)
- AMBER: mm/pbsa error Eric Hu (Wed May 04 2005 - 11:06:34 PDT)
- AMBER: Meaning of induced dipole moments for atom pairs? Cenk Andac (Wed May 04 2005 - 13:52:06 PDT)
- AMBER: How can I read parm99.dat file? Myunggi Yi (Wed May 04 2005 - 16:08:49 PDT)
- Re: AMBER: How can I read parm99.dat file? Bill Ross (Wed May 04 2005 - 17:12:08 PDT)
- AMBER: ibelly in nmode Dawei Zhang (Thu May 05 2005 - 12:23:13 PDT)
- AMBER: problem with gb md emilia wu (Thu May 05 2005 - 19:05:00 PDT)
- AMBER: No vdW parameters for HO.. Vineet Pande (Fri May 06 2005 - 03:20:02 PDT)
- AMBER: a nomenclature question Kenley Barrett (Fri May 06 2005 - 09:11:24 PDT)
- AMBER: Dr. Cornell's calculation of Sulfur vdw epsilon value in parm94.dat? Chris Moth (Fri May 06 2005 - 12:32:23 PDT)
- AMBER: langevin, GB and simulated annealing - 5 pascal.baillod.epfl.ch (Mon May 09 2005 - 09:25:12 PDT)
- AMBER: radial distribution function Myunggi Yi (Mon May 09 2005 - 11:36:43 PDT)
- AMBER: parameter for sulfur in thio-octyl-glucopyranoside Vijay Manickam Achari (Mon May 09 2005 - 20:23:07 PDT)
- Re: AMBER: radius parameter for F atom Scott Pendley (Tue May 10 2005 - 12:49:21 PDT)
- AMBER: AMBER8 Build on Linux x64 running Opterons Thomas Patko (Wed May 11 2005 - 00:10:14 PDT)
- AMBER: Trouble with example tutorial Maciej (Wed May 11 2005 - 04:08:02 PDT)
- AMBER: Parameter for alpha-lactose Sagarika Dev (Wed May 11 2005 - 07:48:21 PDT)
- AMBER: Asking how to creat alanine "dipeptide" in amber8 Li Su (Wed May 11 2005 - 08:37:07 PDT)
- Fwd: Re: AMBER: AMBER Test Anthony Cruz (Wed May 11 2005 - 08:49:38 PDT)
- AMBER: SANDER BOMB: volume of ucell too big Stern, Julie (Wed May 11 2005 - 09:07:38 PDT)
- AMBER: maximum number of processors MURAT CETINKAYA (Wed May 11 2005 - 20:53:44 PDT)
- AMBER: RESP charge fitting for N-methylguanine cation Grzegorz Jezierski (Thu May 12 2005 - 09:50:17 PDT)
- AMBER: Tutorial #1 ptraj/sander problem Daniela Kohen (Thu May 12 2005 - 15:03:07 PDT)
- AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang (Thu May 12 2005 - 18:44:04 PDT)
- AMBER: amber8 test error Cordova, Luis E. (Thu May 12 2005 - 20:26:00 PDT)
- AMBER: creating residues - charge assign problems Hayden Eastwood (Fri May 13 2005 - 04:06:06 PDT)
- AMBER: platinum atom in Xleap Chen Chengwen (Fri May 13 2005 - 19:11:12 PDT)
- AMBER: How to create a parallel job for amber 8? Ò׺ç (Sat May 14 2005 - 04:20:15 PDT)
- AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? caoch.cherry.bio.titech.ac.jp (Sat May 14 2005 - 10:17:17 PDT)
- AMBER: Calculating of radius of gyration in Carnal Hwankyu Lee (Sat May 14 2005 - 11:36:37 PDT)
- Re: AMBER: Calculating of radius of gyration in Carnal Bill Ross (Sat May 14 2005 - 15:26:43 PDT)
- AMBER: how to reduce box size and delete excess solvent hj zou (Sun May 15 2005 - 04:51:32 PDT)
- AMBER: How to set constraint Li Su (Sun May 15 2005 - 11:58:51 PDT)
- Re: AMBER: how to reduce box size and delete excess solvent Bill Ross (Sun May 15 2005 - 12:50:01 PDT)
- AMBER: strange mm_pbsa.pl bug Nelson Fonseca (Mon May 16 2005 - 08:39:21 PDT)
- AMBER: How to set up dihedral constraints in amber Li Su (Mon May 16 2005 - 08:39:50 PDT)
- AMBER: generating over 16 bps of DNA in nucgen Hwankyu Lee (Mon May 16 2005 - 08:33:04 PDT)
- AMBER: output of force field info Stern, Julie (Mon May 16 2005 - 12:24:37 PDT)
- AMBER: nmode in mmpbsa Joseph Fernandez (Mon May 16 2005 - 16:36:28 PDT)
- AMBER: MMPBSA calculations on Highly charged systems Vitor Manuel Sousa F?x (Tue May 17 2005 - 04:01:21 PDT)
- AMBER: Message in .out file Atilio Anzellotti (Tue May 17 2005 - 05:31:36 PDT)
- AMBER: GAFF angle parameters Monica Civera (Tue May 17 2005 - 09:11:46 PDT)
- AMBER: molsurf error mingche Pan (Tue May 17 2005 - 09:52:57 PDT)
- AMBER: compiling pmemd on dual xeon Tiziano Tuccinardi (Tue May 17 2005 - 10:28:31 PDT)
- AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Rajeev Ranjan Singh (Tue May 17 2005 - 13:15:33 PDT)
- AMBER: RE: Tutorial#1 ptraj/sander problem Ross Walker (Tue May 17 2005 - 15:56:59 PDT)
- AMBER: MD on surface Yanze Zhang (Tue May 17 2005 - 16:58:29 PDT)
- AMBER: error with ptraj Xiaowei (David) Li (Tue May 17 2005 - 21:27:33 PDT)
- AMBER: loading pdb cbala.igib.res.in (Tue May 17 2005 - 22:56:13 PDT)
- AMBER: Using AMBER for Carbon nanotubes Zhang Yingyan (Wed May 18 2005 - 01:21:42 PDT)
- AMBER: error during MD run cbala.igib.res.in (Wed May 18 2005 - 11:39:25 PDT)
- AMBER: frcmod info for Nickel Kara Di Giorgio (Wed May 18 2005 - 12:04:44 PDT)
- AMBER: parameter for sulfur in thio-glucoside residue Vijay Manickam Achari (Wed May 18 2005 - 18:58:57 PDT)
- AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim (Wed May 18 2005 - 19:16:35 PDT)
- AMBER: Amber 8 and LAM compilation problem Glen Otero (Wed May 18 2005 - 22:52:00 PDT)
- AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Vijay Manickam Achari (Wed May 18 2005 - 23:55:21 PDT)
- AMBER: GB - igb=1 versus dielc=? milion.c-box.cz (Thu May 19 2005 - 09:53:00 PDT)
- AMBER: write format of restart crd in sander/pmemd Peter Varnai (Thu May 19 2005 - 05:12:22 PDT)
- AMBER: Using amber4 generated prep files in amber8? Simon Whitehead (Thu May 19 2005 - 05:51:00 PDT)
- AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 18:19:04 PDT)
- AMBER: MM_PBSA for NMR restrained structures Cenk Andac (Fri May 20 2005 - 01:36:10 PDT)
- AMBER: Representation of cations in MD Thomas Steinbrecher (Fri May 20 2005 - 02:30:24 PDT)
- AMBER: leap problem: savepdb Hannes Barsch (Fri May 20 2005 - 02:30:29 PDT)
- AMBER: how to creat leaprc.gaff Vijay Manickam Achari (Fri May 20 2005 - 02:36:25 PDT)
- AMBER: Error in minimization Priti Hansia (Fri May 20 2005 - 03:58:36 PDT)
- AMBER: Steve Seibold (Fri May 20 2005 - 10:45:24 PDT)
- AMBER: crashing xleap Kenley Barrett (Fri May 20 2005 - 11:48:13 PDT)
- AMBER: 1-4 scaling factors Stern, Julie (Fri May 20 2005 - 12:13:22 PDT)
- Re: AMBER: crashing xleap Bill Ross (Fri May 20 2005 - 12:55:15 PDT)
- AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Sun May 22 2005 - 12:44:55 PDT)
- AMBER: Copyright for PBSA Cenk Andac (Sat May 21 2005 - 01:32:00 PDT)
- AMBER: Citing the PBSA module of AMBER8 Cenk Andac (Fri May 20 2005 - 14:27:03 PDT)
- AMBER: rotating and repositioning molecules in xleap Hwankyu Lee (Fri May 20 2005 - 23:09:45 PDT)
- AMBER: modeller Zhang Bing (Fri May 20 2005 - 21:53:13 PDT)
- Re: AMBER: Unexpected stop of Sander run Bill Ross (Sun May 22 2005 - 13:18:16 PDT)
- AMBER: Error in sander: stack trace terminated abnormally. Hwankyu Lee (Sun May 22 2005 - 14:05:31 PDT)
- AMBER: antechamber not working .. for thio residue.. Vijay Manickam Achari (Sun May 22 2005 - 19:15:20 PDT)
- AMBER: Setting Amber force field parameters Chen Chengwen (Mon May 23 2005 - 00:55:38 PDT)
- AMBER: using antechamber ... to get prepin file Vijay Manickam Achari (Mon May 23 2005 - 01:59:16 PDT)
- AMBER: Connecting two molecules Hwankyu Lee (Mon May 23 2005 - 08:13:00 PDT)
- AMBER: how to generate frcmod file for using prepin file.. Vijay Manickam Achari (Mon May 23 2005 - 19:52:18 PDT)
- AMBER: my frcmod file created using parmchk Vijay Manickam Achari (Mon May 23 2005 - 20:44:21 PDT)
- AMBER: my prepin file in lowe-case Vijay Manickam Achari (Tue May 24 2005 - 00:51:55 PDT)
- AMBER: Which forcefield? Simon Whitehead (Tue May 24 2005 - 01:13:01 PDT)
- AMBER: conformational sampling of a peptide Hannes Barsch (Tue May 24 2005 - 01:58:04 PDT)
- AMBER: amber code Juan Fernandez Carmona (Tue May 24 2005 - 03:08:00 PDT)
- Re: AMBER: conformational sampling of a peptide Carlos Simmerling (Tue May 24 2005 - 06:11:53 PDT)
- AMBER: Fw: Installing PMEMD on IBM machine (CPU power4) running SUSE_9.1 Robert Duke (Tue May 24 2005 - 07:42:15 PDT)
- AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_' René Ranzinger (Tue May 24 2005 - 08:04:42 PDT)
- AMBER: Sander Restart Problem Garhan Attebury (Tue May 24 2005 - 08:07:49 PDT)
- AMBER: How to fix certain bond angles Li Su (Tue May 24 2005 - 08:27:14 PDT)
- AMBER: Error: vlimit exceeded for step Hwankyu Lee (Tue May 24 2005 - 10:20:10 PDT)
- Solute-solvent boundary in pbsa ..Re: AMBER: Copyright for PBSA Cenk Andac (Tue May 24 2005 - 11:48:26 PDT)
- AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Li Su (Tue May 24 2005 - 12:14:09 PDT)
- AMBER: charges difference of atom in xleap and prmtop chaiann ng (Tue May 24 2005 - 21:02:33 PDT)
- AMBER: PARMSCAN program Philippe ARNAUD (Wed May 25 2005 - 00:28:31 PDT)
- AMBER: average structure after MD kuljeets.igib.res.in (Wed May 25 2005 - 02:14:19 PDT)
- AMBER: quadrupole in resp riccardo nifosi (Wed May 25 2005 - 03:44:20 PDT)
- AMBER: error in chirality.c? Kenley Barrett (Wed May 25 2005 - 07:27:07 PDT)
- Re#2:Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac (Wed May 25 2005 - 13:03:47 PDT)
- AMBER: dissolving micelle structure in water.. amber7 Vijay Manickam Achari (Wed May 25 2005 - 20:59:22 PDT)
- AMBER: distance restraints between two centers of mass JAVIER PEREZ (Thu May 26 2005 - 01:37:30 PDT)
- AMBER: Is the MD simulation normal Shulin Zhuang (Thu May 26 2005 - 08:30:48 PDT)
- AMBER: setting up Parallel processing mathew k varghese (Thu May 26 2005 - 08:39:00 PDT)
- AMBER: hbond analysis in ptaj/carnal Jana Precechtelova (Thu May 26 2005 - 09:25:20 PDT)
- Re: AMBER: hbond analysis in ptaj/carnal Bill Ross (Thu May 26 2005 - 09:44:13 PDT)
- AMBER: why is snaupe.f is empty? Cordova, Luis E. (Thu May 26 2005 - 10:06:24 PDT)
- AMBER: ptraj - hbond detailed analysis over time? pascal.baillod.epfl.ch (Thu May 26 2005 - 10:38:38 PDT)
- AMBER: Mol2 to prepin file conversion Andrew Box (Thu May 26 2005 - 17:08:22 PDT)
- AMBER: question about loadiing pdb file of a molecule complex gtg549i.mail.gatech.edu (Fri May 27 2005 - 14:39:28 PDT)
- AMBER: Workshop Tutorials Downtime this weekend. Ross Walker (Fri May 27 2005 - 14:49:05 PDT)
- AMBER: Antechamber RESP failed for large organic molecule junwang (Sun May 29 2005 - 12:57:59 PDT)
- AMBER: question about initial conditions for amber Ed Pate (Sun May 29 2005 - 19:42:21 PDT)
- AMBER: density profiles in ptraj or carnal Hwankyu Lee (Sun May 29 2005 - 20:27:37 PDT)
- AMBER: pairwise energy decomposition using MM-PBSA Xin Hu (Sun May 29 2005 - 20:38:30 PDT)
- AMBER: Force field modification problem yuann (Mon May 30 2005 - 04:16:27 PDT)
- AMBER: Bond angle restraints setting files Li Su (Mon May 30 2005 - 09:05:15 PDT)
- Re: AMBER: density profiles in ptraj or carnal Bill Ross (Mon May 30 2005 - 10:00:08 PDT)
- AMBER: density problem cristian obiol (Tue May 31 2005 - 02:17:46 PDT)
- AMBER: stack terminated abnormally drugdesign (Tue May 31 2005 - 03:20:33 PDT)
- AMBER: if setting ntf=4, will it cause someproblem? Li Su (Tue May 31 2005 - 07:55:03 PDT)
- AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Tue May 31 2005 - 08:23:51 PDT)
- AMBER: DNA base-flipping: TI vs PMF Lauren O'Neil (Tue May 31 2005 - 08:40:45 PDT)
- AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Grzegorz Jezierski (Tue May 31 2005 - 09:04:20 PDT)
- AMBER: MM-PBSA calculation masi.nmr.mpibpc.mpg.de (Tue May 31 2005 - 09:37:40 PDT)
- AMBER: STOP 0 masi.nmr.mpibpc.mpg.de (Tue May 31 2005 - 09:40:25 PDT)
- AMBER:Sander errors: Unit 6 Error on OPEN: mdout Douali, Latifa (Tue May 31 2005 - 10:34:41 PDT)
- Re: AMBER: STOP 0 Bill Ross (Tue May 31 2005 - 10:43:32 PDT)
- AMBER: meaningful tax for sander question Cordova, Luis E. (Tue May 31 2005 - 12:19:30 PDT)
- AMBER: double counting of potentials Stern, Julie (Tue May 31 2005 - 16:04:43 PDT)
- AMBER: Working with a nickel-organometallic compound Kara Di Giorgio (Tue May 31 2005 - 16:36:30 PDT)
- AMBER: External Field in AMBER? junwang (Tue May 31 2005 - 19:19:38 PDT)
- Last message date: Wed Jun 01 2005 - 04:53:00 PDT
- Archived on: Sun Mar 14 2010 - 05:59:23 PDT
