Amber Archive Apr 2005 by thread
- AMBER: GB dynamics mathew k varghese (Thu Mar 31 2005 - 20:01:30 PST)
- AMBER: solvateoct mymolecule CHCL3BOX 10 PROBLEM!!! chaiann ng (Thu Mar 31 2005 - 20:30:40 PST)
- AMBER: How to fix the torsion angles during energy minimization Ananda Rama Krishnan Selvaraj (Thu Mar 31 2005 - 22:42:27 PST)
- AMBER: scaleCharges with polarisable force fields Phineus Markwick (Fri Apr 01 2005 - 04:57:43 PST)
- AMBER: Problems with protonate on Linux Atro Tossavainen (Fri Apr 01 2005 - 05:09:32 PST)
- AMBER: reference of Targeted MD xhu1.memphis.edu (Fri Apr 01 2005 - 13:52:59 PST)
- Re: AMBER: GB dynamics Bill Ross (Fri Apr 01 2005 - 13:55:07 PST)
- AMBER: oxo-heme Peter Gannett (Fri Apr 01 2005 - 14:32:47 PST)
- Re: AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS Robert Duke (Sat Apr 02 2005 - 16:42:47 PST)
- AMBER: problem with input files when using ff02EP + pol3 Phineus Markwick (Sun Apr 03 2005 - 05:35:28 PDT)
- Re: AMBER: All the tests passed except prmtop and prepin... shuli (Sun Apr 03 2005 - 08:24:47 PDT)
- AMBER: helical parameters obtaining Kateryna Miroshnychenko (Sat Apr 02 2005 - 03:08:17 PST)
- AMBER: surface area John (Mon Apr 04 2005 - 03:35:58 PDT)
- AMBER: Sander minimization & dynamic question chaiann ng (Mon Apr 04 2005 - 03:45:48 PDT)
- AMBER: ff02EP + pol3 (2) Phineus Markwick (Mon Apr 04 2005 - 05:06:36 PDT)
- AMBER: emilia wu (Mon Apr 04 2005 - 07:11:48 PDT)
- AMBER: single-stranded poly(rC) simulation Kateryna Miroshnychenko (Mon Apr 04 2005 - 06:49:39 PDT)
- AMBER: force constant Unit used in TMD xhu1.memphis.edu (Mon Apr 04 2005 - 08:05:30 PDT)
- AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters Wu Yingliang (Mon Apr 04 2005 - 23:18:11 PDT)
- AMBER: AMBER 8.0 problems with impose (tleap) on linux Guillermo Mulliert Carlín (Mon Apr 04 2005 - 23:35:17 PDT)
- AMBER: how to make a nonsymmetric box around the solute Lina Nilsson (Tue Apr 05 2005 - 00:56:44 PDT)
- AMBER: doble C and N terminal Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Tue Apr 05 2005 - 02:45:58 PDT)
- AMBER: GB with Langevin dynamics problem Peter Varnai (Tue Apr 05 2005 - 09:04:15 PDT)
- AMBER: Re:Re:single-stranded poly(rC) simulation Kateryna Miroshnychenko (Tue Apr 05 2005 - 10:37:54 PDT)
- AMBER: Protein with structural ions Kara Wald (Tue Apr 05 2005 - 14:29:46 PDT)
- AMBER: FW: Amber installation Eric Mullins (Wed Apr 06 2005 - 08:36:20 PDT)
- AMBER: a bimolecular reaction Eric Hu (Wed Apr 06 2005 - 10:14:23 PDT)
- AMBER: About Gaussian Key Words Katagiri Daisuke (Wed Apr 06 2005 - 20:10:12 PDT)
- AMBER: value of SALTCON mathew k varghese (Wed Apr 06 2005 - 21:29:01 PDT)
- AMBER: combine mdcrd using ptraj xueping (Wed Apr 06 2005 - 21:41:48 PDT)
- AMBER: RADIOPT=1 Fabien Cailliez (Thu Apr 07 2005 - 06:19:09 PDT)
- AMBER: RE: system comparison for amber Ross Walker (Thu Apr 07 2005 - 09:41:06 PDT)
- AMBER: leap single precision Guanglei Cui (Thu Apr 07 2005 - 11:04:20 PDT)
- Re: AMBER: About Gaussian Key Words (fwd) duan_list.albert.genomecenter.ucdavis.edu (Thu Apr 07 2005 - 16:09:25 PDT)
- AMBER: makeDIST_RST ERROR Y. Xu (Thu Apr 07 2005 - 19:14:19 PDT)
- AMBER: problems with "protonate" Kenley Barrett (Thu Apr 07 2005 - 19:27:07 PDT)
- AMBER: how to get the parameters for modified amino acid residue? ying xiong (Thu Apr 07 2005 - 20:31:14 PDT)
- AMBER: linit in mm-pbsa Fabien Cailliez (Fri Apr 08 2005 - 02:08:52 PDT)
- AMBER: Disulfide bond michael chen (Fri Apr 08 2005 - 07:36:41 PDT)
- AMBER: GB with Langevin dynamics problem 2 Peter Varnai (Fri Apr 08 2005 - 09:29:08 PDT)
- AMBER: Announcment: Nucleic Acid Builder (NAB) version 5 is released David A. Case (Fri Apr 08 2005 - 09:52:54 PDT)
- AMBER: question about TGMD: vlimit exceeded for step xhu1.memphis.edu (Fri Apr 08 2005 - 13:31:10 PDT)
- AMBER: average structure-ptraj xueping (Sat Apr 09 2005 - 01:23:23 PDT)
- AMBER: A question on connecting residues in xleap Hwankyu Lee (Sun Apr 10 2005 - 09:54:55 PDT)
- AMBER: Warnings as a file Pavan Ghatty (Sun Apr 10 2005 - 21:37:21 PDT)
- AMBER: Two question about dielectric constant 烨 武 (Mon Apr 11 2005 - 01:02:10 PDT)
- AMBER: rst file problems mathew k varghese (Mon Apr 11 2005 - 03:03:41 PDT)
- AMBER:FAD can't be minimized. zhli_2000.126.com (Mon Apr 11 2005 - 05:48:15 PDT)
- AMBER: MM_PBSA error Xin Hu (Mon Apr 11 2005 - 11:46:30 PDT)
- AMBER: breaking symmetry in minimization Stern, Julie (Mon Apr 11 2005 - 13:58:53 PDT)
- Re: AMBER: breaking symmetry in minimization Bill Ross (Mon Apr 11 2005 - 15:25:25 PDT)
- AMBER: Fail to load the trajectory file. Jinzhi Lei (Mon Apr 11 2005 - 17:36:34 PDT)
- Re: AMBER: Fail to load the trajectory file. Bill Ross (Mon Apr 11 2005 - 17:41:52 PDT)
- AMBER: peptide side chain modification with LEAP Hannes Barsch (Tue Apr 12 2005 - 07:19:53 PDT)
- AMBER: implementing AMBER in NAMD Lina Nilsson (Thu Apr 28 2005 - 07:23:16 PDT)
- AMBER: Does anybody know the experimental solvation free energies of Efavirenz and some other DPC drugs Ye MEI (Tue Apr 12 2005 - 08:19:37 PDT)
- Re: AMBER: peptide side chain modification with LEAP Bill Ross (Tue Apr 12 2005 - 09:22:40 PDT)
- AMBER: Silicon related parameters luckyang.gmail.com (Tue Apr 12 2005 - 09:38:35 PDT)
- AMBER: ibelly not working Stern, Julie (Tue Apr 12 2005 - 09:52:56 PDT)
- AMBER: vdw or center box dimensions, periodicity, and the jagged edge Stern, Julie (Tue Apr 12 2005 - 10:30:38 PDT)
- AMBER: Protein With Structural Ions Kara Di Giorgio (Tue Apr 12 2005 - 10:47:52 PDT)
- AMBER: No. of Snapshots in MM/GB/SA Sagar D Khare (Tue Apr 12 2005 - 10:48:44 PDT)
- Re: AMBER: ibelly not working Bill Ross (Tue Apr 12 2005 - 11:11:28 PDT)
- AMBER: ptraj, hbond problem Joseph W.Toporowski (Tue Apr 12 2005 - 17:07:35 PDT)
- AMBER: MM-PBSA in protein-Zn-ligand system Yong Xu (Tue Apr 12 2005 - 18:37:55 PDT)
- AMBER: freee energy calculation without minimised structure S.Sundar Raman (Wed Apr 13 2005 - 00:00:08 PDT)
- AMBER: Watson-Crick restraints YoungJin Cho (Wed Apr 13 2005 - 07:43:22 PDT)
- AMBER: what is wrong with my amber job or installation? Amber (Wed Apr 13 2005 - 11:57:56 PDT)
- AMBER: Formatting a restraint file Kara Wald (Wed Apr 13 2005 - 13:57:24 PDT)
- AMBER: xleap, lib file question opitz.che.udel.edu (Wed Apr 13 2005 - 14:36:51 PDT)
- AMBER: solvate water box bybaker.itsa.ucsf.edu (Wed Apr 13 2005 - 23:42:21 PDT)
- AMBER: Antechamber -reorders atom sequence Austin B. Yongye (Thu Apr 14 2005 - 05:05:09 PDT)
- AMBER: Warning: Error opening "New" file from subroutine OPNMRG in pmemd Fabien Cailliez (Thu Apr 14 2005 - 06:05:32 PDT)
- AMBER: periodic boundaries and repeating structure Stern, Julie (Thu Apr 14 2005 - 10:55:09 PDT)
- AMBER: antechamber for cyano group nlxc (Thu Apr 14 2005 - 11:03:35 PDT)
- Re: AMBER: periodic boundaries and repeating structure Bill Ross (Thu Apr 14 2005 - 11:13:48 PDT)
- AMBER: Sander/Mpich2 error with mpd_singinit Joe Nolan (Thu Apr 14 2005 - 13:00:09 PDT)
- AMBER: small target pressure in constant pressure dynamics Eric Hu (Thu Apr 14 2005 - 14:37:49 PDT)
- AMBER: big fluctuation in MM-PBSA/GA Eric Hu (Thu Apr 14 2005 - 15:54:05 PDT)
- AMBER: parameters in gaff.dat Lihua Wang (Thu Apr 14 2005 - 22:21:29 PDT)
- AMBER: how to make the prepin file for dimer and clusters of organic molecule in Amber7 Ananda Rama Krishnan Selvaraj (Fri Apr 15 2005 - 01:11:27 PDT)
- AMBER: carnal problem Ed Pate (Fri Apr 15 2005 - 09:15:54 PDT)
- AMBER: SollvateBox with ethanol Huaer XC (Fri Apr 15 2005 - 09:21:01 PDT)
- AMBER: gaff atom types Claudio Morgado (Fri Apr 15 2005 - 10:11:18 PDT)
- Re: AMBER: carnal problem Bill Ross (Fri Apr 15 2005 - 10:32:02 PDT)
- AMBER: RESP charges with Gaussian03 and Amber Delon Wilson (Fri Apr 15 2005 - 13:57:19 PDT)
- AMBER: the restart of replica exchange method (REM) simulations in AMBER8 Scott E. Boesch (Fri Apr 15 2005 - 14:24:24 PDT)
- AMBER: about equilibration dynamics S.Sundar Raman (Mon Apr 18 2005 - 00:18:10 PDT)
- AMBER: ATTN REVISION 吕海婷 (Mon Apr 18 2005 - 01:19:46 PDT)
- AMBER: dielectric constant Nina Fischer (Mon Apr 18 2005 - 01:22:34 PDT)
- AMBER:Bond lengths aren't reasonable after minimisation. zhli_2000.126.com (Mon Apr 18 2005 - 03:39:22 PDT)
- AMBER: Rep Exch. suggestion Brent Krueger (Mon Apr 18 2005 - 04:56:33 PDT)
- AMBER: langevin, GB and simulated annealing? pascal.baillod.epfl.ch (Mon Apr 18 2005 - 08:14:08 PDT)
- AMBER: Dual Xeon EM64T Intel Fortran Compiler Shekter, Lee (Mon Apr 18 2005 - 11:17:58 PDT)
- AMBER: local dielectric constant Xavier Deupi (Mon Apr 18 2005 - 18:17:40 PDT)
- AMBER: Re: Re: AMBER: ATTN REVISION 吕海婷 (Mon Apr 18 2005 - 18:38:02 PDT)
- AMBER: RESP charges - multiple conformations Austin B. Yongye (Mon Apr 18 2005 - 19:54:20 PDT)
- AMBER: New parametrs Maciej (Mon Apr 18 2005 - 22:38:51 PDT)
- AMBER: GAFF: H type on carbon bearing a cyano group Claudio Morgado (Tue Apr 19 2005 - 01:34:12 PDT)
- AMBER: Gibbs compilation problem Maciej (Tue Apr 19 2005 - 04:36:52 PDT)
- AMBER: solvent accessible surface area John (Tue Apr 19 2005 - 03:45:40 PDT)
- AMBER: Amber8 installation on IBM (power4) with SUSE 9.1 Linux (IBM XLF compiler) Soo Joo (Tue Apr 19 2005 - 02:36:26 PDT)
- AMBER: a problem with mm_pbsa Ye MEI (Tue Apr 19 2005 - 07:23:01 PDT)
- AMBER: Amber compilation problem David A. Case (Tue Apr 19 2005 - 07:59:27 PDT)
- AMBER: Non-Bonded Cutoff vs PME Vineet Pande (Tue Apr 19 2005 - 09:13:26 PDT)
- AMBER: Yong Xu (Tue Apr 19 2005 - 19:57:44 PDT)
- AMBER: tleap and water thenmalar (Wed Apr 20 2005 - 01:13:58 PDT)
- AMBER: GB and mm_pbsa.pl Nelson Fonseca (Wed Apr 20 2005 - 04:48:48 PDT)
- AMBER: interaction between residues Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Wed Apr 20 2005 - 07:27:31 PDT)
- AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. zhli_2000 (Wed Apr 20 2005 - 06:52:18 PDT)
- AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. Ross Walker (Wed Apr 20 2005 - 10:04:03 PDT)
- AMBER: ibelly not working Stern, Julie (Wed Apr 20 2005 - 12:40:28 PDT)
- AMBER: intramolecular nonbonded interactions in AMBER force field John Silvio Vieceli (Wed Apr 20 2005 - 15:06:48 PDT)
- AMBER: about run time in GB and PB Yong Xu (Thu Apr 21 2005 - 01:06:27 PDT)
- AMBER: On the role of neutralizing ions in GB-MD and GBSA Wu Yingliang (Thu Apr 21 2005 - 03:26:05 PDT)
- AMBER: On the role of neutralizing ions in GB-MD and GBSA Wu Yingliang (Thu Apr 21 2005 - 03:16:29 PDT)
- AMBER: Nose-Hoover thermostat Sam Moors (Thu Apr 21 2005 - 05:40:44 PDT)
- AMBER: re: about run time in GB and PB Phineus Markwick (Thu Apr 21 2005 - 07:29:33 PDT)
- AMBER: Moil-view and Quicktime movie Steve Seibold (Thu Apr 21 2005 - 07:55:01 PDT)
- AMBER: Sander bomb - atom out of bounds Joe Nolan (Thu Apr 21 2005 - 10:46:01 PDT)
- AMBER: problem with belly calculation restart Ed Pate (Thu Apr 21 2005 - 17:28:59 PDT)
- AMBER: mean structure calculation mmv (Fri Apr 22 2005 - 02:17:20 PDT)
- AMBER: PB Bomb in circle(): Stored surface points over limit Nelson Fonseca (Fri Apr 22 2005 - 05:56:57 PDT)
- AMBER: writing MASKs Sagar D Khare (Fri Apr 22 2005 - 07:58:24 PDT)
- AMBER: strange VDWAALS and EEL energies calculated by pbsa Fabien Cailliez (Fri Apr 22 2005 - 08:56:41 PDT)
- AMBER: Induced dipole in AMBER8 Cenk Andac (Fri Apr 22 2005 - 09:57:56 PDT)
- AMBER: Amber Installation pmullins (Fri Apr 22 2005 - 11:28:34 PDT)
- AMBER: Calculate vdw parameters for alkaline earth metal ions Kenley Barrett (Fri Apr 22 2005 - 15:19:23 PDT)
- Re: AMBER: Calculate vdw parameters for alkaline earth metal ions Bill Ross (Fri Apr 22 2005 - 15:48:15 PDT)
- AMBER: Problem when converting AMBER trajectories to CHARMM format Chen Hu (Sat Apr 23 2005 - 15:20:56 PDT)
- AMBER: serial and parallel Aknb (Sun Apr 24 2005 - 04:35:37 PDT)
- AMBER: coordinates translation Ye MEI (Sun Apr 24 2005 - 09:26:39 PDT)
- AMBER: AMBER Test Error tpatko (Sun Apr 24 2005 - 17:31:42 PDT)
- AMBER: How to deal with the Non-standard residue lv haiting (Mon Apr 25 2005 - 01:18:08 PDT)
- AMBER: the restarting error zhli_2000.126.com (Mon Apr 25 2005 - 07:08:02 PDT)
- AMBER: Free energy pertubation (thermodynamic intergration) mrbroad.ilstu.edu (Mon Apr 25 2005 - 09:20:35 PDT)
- AMBER: radius parameter for F atom Ye MEI (Mon Apr 25 2005 - 10:05:06 PDT)
- AMBER: mm_pbsa problem Husni Fattayer (Mon Apr 25 2005 - 13:59:22 PDT)
- AMBER: A problem in TI approach - test case: meth2eth and eth2meth Ilyas Yildirim (Mon Apr 25 2005 - 18:47:19 PDT)
- AMBER: Free energy Maciej (Tue Apr 26 2005 - 00:01:16 PDT)
- AMBER: Re:Gibbs compilation problem Maciej (Tue Apr 26 2005 - 00:05:31 PDT)
- AMBER: langevin, GB and simulated annealing - 3 pascal.baillod.epfl.ch (Tue Apr 26 2005 - 03:37:16 PDT)
- AMBER: AMBER Test Anthony Cruz (Tue Apr 26 2005 - 03:36:27 PDT)
- AMBER: doesn't work in pmemd, and no output in parallel simulations Hwankyu Lee (Tue Apr 26 2005 - 13:35:26 PDT)
- AMBER: error in pbsa calculation mingche Pan (Tue Apr 26 2005 - 14:15:13 PDT)
- AMBER: capping amit.mbu.iisc.ernet.in (Wed Apr 27 2005 - 00:30:37 PDT)
- AMBER: emilia wu (Wed Apr 27 2005 - 19:35:59 PDT)
- Re: AMBER: Pyranose pucker parameters Thomas E. Cheatham, III (Wed Apr 27 2005 - 20:57:26 PDT)
- AMBER: mixture solvent model Huaer XC (Wed Apr 27 2005 - 21:13:11 PDT)
- AMBER: distance restraints mathew k varghese (Thu Apr 28 2005 - 00:00:16 PDT)
- AMBER: Problem with "Thermodynamic integration calculations" tutorial ,unsuspected error Maciej (Thu Apr 28 2005 - 00:41:21 PDT)
- AMBER: false bond created upon coordinate retrieval Stern, Julie (Thu Apr 28 2005 - 14:29:38 PDT)
- Re: AMBER: false bond created upon coordinate retrieval Bill Ross (Thu Apr 28 2005 - 15:00:38 PDT)
- AMBER: segmentation problem aanzellotti.mail2.vcu.edu (Thu Apr 28 2005 - 16:46:36 PDT)
- AMBER: Re: R.E.D. question FyD (Fri Apr 29 2005 - 13:21:34 PDT)
- AMBER: Odd Antechamber Behavior Kara Di Giorgio (Fri Apr 29 2005 - 21:48:01 PDT)
- AMBER: ipol=1 & use_pme= ?? Cenk Andac (Sat Apr 30 2005 - 06:26:57 PDT)
- Last message date: Sat Apr 30 2005 - 14:53:00 PDT
- Archived on: Mon Dec 23 2024 - 05:53:21 PST
