Amber Archive Sep 2008 by thread
- AMBER: tleap and Zn parameter Aust, Susanne (Mon Sep 01 2008 - 01:14:53 PDT)
- AMBER: ptraj and netcdf with AmberTools1.2 ? Lars Skjærven (Mon Sep 01 2008 - 02:11:23 PDT)
- Re: AMBER: RE: Personal favor fatima.chami.durham.ac.uk (Mon Sep 01 2008 - 04:29:46 PDT)
- Re: AMBER: solvent interaction in active site Carlos Simmerling (Mon Sep 01 2008 - 06:49:20 PDT)
- AW: AMBER: tleap and Zn parameter Aust, Susanne (Mon Sep 01 2008 - 23:46:23 PDT)
- Re: AMBER: compilation problem john smith (Tue Sep 02 2008 - 03:03:14 PDT)
- AMBER: mmpbsa Henrik Öberg (Tue Sep 02 2008 - 04:36:55 PDT)
- AMBER: AMBER9 installation problen with open mpi saurabh agrawal (Tue Sep 02 2008 - 04:41:55 PDT)
- AMBER: ptraj & imaging of velocities FyD (Tue Sep 02 2008 - 06:06:08 PDT)
- AMBER: a question about matrix command? TaoPaul (Tue Sep 02 2008 - 18:01:04 PDT)
- AMBER: MM_PBSA - SASA - Question Deepangi Pandit (Tue Sep 02 2008 - 19:10:13 PDT)
- AW: AMBER: tleap and Zn parameter Aust, Susanne (Wed Sep 03 2008 - 00:18:28 PDT)
- AMBER: Need help... High energies for complex... Waqas Nasir (Wed Sep 03 2008 - 04:20:01 PDT)
- AMBER: help...ptraj does not output bounding box info Jose Borreguero (Wed Sep 03 2008 - 08:39:41 PDT)
- AMBER: Marisa Frechero (Wed Sep 03 2008 - 11:38:06 PDT)
- AMBER: matrix correl Steve Seibold (Wed Sep 03 2008 - 11:40:28 PDT)
- AMBER: nmode units Arturas Ziemys (Wed Sep 03 2008 - 15:28:44 PDT)
- AMBER: mmpbsa molsurf.c error Ilyas Yildirim (Wed Sep 03 2008 - 16:56:59 PDT)
- AMBER: No bond and angle parameters for - -????? Waqas Nasir (Thu Sep 04 2008 - 03:15:37 PDT)
- AMBER: Need help... High energies for complex... Waqas Nasir (Thu Sep 04 2008 - 03:38:53 PDT)
- AMBER: antechamber cannot generate prep files moitrayee.mbu.iisc.ernet.in (Thu Sep 04 2008 - 04:47:17 PDT)
- AMBER: help... structure factors from amber trajectories? Jose Borreguero (Thu Sep 04 2008 - 10:35:57 PDT)
- Re: AMBER: xleap fails to savemol2 FyD (Thu Sep 04 2008 - 12:45:49 PDT)
- AMBER: resp and 99999 Markus Kaukonen (Thu Sep 04 2008 - 23:13:10 PDT)
- AMBER: help...sander "segmentation fault" after 2hours of minimization Jose Borreguero (Fri Sep 05 2008 - 08:06:42 PDT)
- AMBER: error when using tleap with leaprc.ff02EP Yongmei Pan (Fri Sep 05 2008 - 08:49:38 PDT)
- AMBER: RE: reference paper - pls help Ross Walker (Fri Sep 05 2008 - 09:37:24 PDT)
- AMBER: mm_pbsa error : Scale paremeter for PBSA CHAMI F. (Fri Sep 05 2008 - 10:26:46 PDT)
- AMBER: ESURF - SASA - isolate residues Deepangi Pandit (Fri Sep 05 2008 - 07:23:23 PDT)
- AMBER: Problem in EVB and Trajectory analysis sai kumar ramadugu (Fri Sep 05 2008 - 14:20:17 PDT)
- AMBER: Explanation of the energy unit ? Marek Malý (Sat Sep 06 2008 - 07:29:06 PDT)
- AMBER: Test error in installing amber 10 using four threads on a single-cpu machine haixiao jin (Sun Sep 07 2008 - 02:42:10 PDT)
- AMBER: PMEMD installation problem. Cenk \(Jenk\) Andac (Sun Sep 07 2008 - 23:58:42 PDT)
- AMBER: amber minimisation Majeed Shaik (Mon Sep 08 2008 - 05:32:17 PDT)
- AMBER: Changes in the Amber web site David A. Case (Mon Sep 08 2008 - 06:25:41 PDT)
- AMBER: problem when running energy minimization with polarizable potential Yongmei Pan (Mon Sep 08 2008 - 08:32:30 PDT)
- AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors Ben Roberts (Mon Sep 08 2008 - 08:43:47 PDT)
- AMBER: Another problem when trying to compile Sander in debug mode Ben Roberts (Mon Sep 08 2008 - 08:49:52 PDT)
- Re: AMBER: Is there a way to cluster frames of a trajectory? Sasha Buzko (Mon Sep 08 2008 - 13:34:22 PDT)
- AMBER: who can give a sample input file regarding the energy decomposition with sander? Yongmei Pan (Mon Sep 08 2008 - 13:41:37 PDT)
- AMBER: NAB parameter: wcons ramu.vt.edu (Mon Sep 08 2008 - 14:06:54 PDT)
- AMBER: energy decomposition with sander? Yongmei Pan (Mon Sep 08 2008 - 14:32:32 PDT)
- Re: AMBER: Using AMBER forces Germain Vallverdu (Tue Sep 09 2008 - 06:48:32 PDT)
- AMBER: PMEMD and sander.MPI Germain Vallverdu (Tue Sep 09 2008 - 06:50:40 PDT)
- AMBER: Amber10 Compilation Anthony Cruz (Tue Sep 09 2008 - 07:26:04 PDT)
- AMBER: about NMR refinement in explicit solvent Rogelio Hernández (Tue Sep 09 2008 - 12:15:19 PDT)
- AMBER: Emperical Valence Bond sai kumar ramadugu (Tue Sep 09 2008 - 14:46:25 PDT)
- AMBER: Preparing peptides with D-amino acids David Watson (Tue Sep 09 2008 - 17:06:58 PDT)
- AMBER: RDF: Segmentation fault Sergey Samsonov (Wed Sep 10 2008 - 01:13:29 PDT)
- AMBER: steered MD Germain Vallverdu (Wed Sep 10 2008 - 03:26:31 PDT)
- AMBER: Cutoff list exceeds largest sphere in unit cell Majeed Shaik (Wed Sep 10 2008 - 07:54:58 PDT)
- AMBER: Nonbonded FE parameter missing in frcmod. moitrayee.mbu.iisc.ernet.in (Thu Sep 11 2008 - 05:22:58 PDT)
- AMBER: Help...which commands in ptraj does clustering by RMSD? Jose Borreguero (Thu Sep 11 2008 - 13:28:49 PDT)
- AMBER: EVB allocation problem sai kumar ramadugu (Fri Sep 12 2008 - 09:08:41 PDT)
- AMBER: Comment: constant pH, non-integer charge -> weird error Markus Kaukonen (Sun Sep 14 2008 - 00:51:58 PDT)
- AMBER: mulliken charges in QM/MM calculation Barbault Florent (Sun Sep 14 2008 - 01:26:25 PDT)
- AMBER: Failure of antechamber in amber10 Francesco Pietra (Sun Sep 14 2008 - 07:18:49 PDT)
- AMBER: problem in installing parallel version of amber10 with lam Shibasish Chowdhury (Sun Sep 14 2008 - 21:20:12 PDT)
- AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in (Sun Sep 14 2008 - 23:35:39 PDT)
- AMBER: question about dihedral angles Harry (Yicun) Ni (Mon Sep 15 2008 - 07:41:31 PDT)
- AMBER: Hydrogen bond energies in explicit solvent. Waqas Nasir (Mon Sep 15 2008 - 07:56:34 PDT)
- AMBER: Minimizaton stops after Ncyc steps only mon_sharma.research.iiit.ac.in (Mon Sep 15 2008 - 09:34:22 PDT)
- AMBER: Announcement of ACS COMP Division CCG and HP award deadlines for Spring 2009 meeting Carlos Simmerling (Mon Sep 15 2008 - 09:39:58 PDT)
- AMBER: parallel amber 10 sander.MPI (low cpu utilization) meandme meandme (Mon Sep 15 2008 - 10:27:06 PDT)
- AMBER: amber 10 parallel cpu utlization meandme meandme (Mon Sep 15 2008 - 10:30:49 PDT)
- AMBER: AMBER10 Compilation (SGI Altix) Anthony Cruz (Mon Sep 15 2008 - 11:21:49 PDT)
- AMBER: MM-PBSA/NMODE in Amber 10 Peterson, Matthew W. (MPETERSON) (Mon Sep 15 2008 - 13:37:41 PDT)
- AMBER: Temperature regulation julliane Yoneda (Mon Sep 15 2008 - 17:48:50 PDT)
- AMBER: top and crd files without hydrogen Waqas Nasir (Tue Sep 16 2008 - 02:18:08 PDT)
- AMBER: nmode/nab entropy calculations memory issues chaitanya koppisetty (Tue Sep 16 2008 - 07:58:01 PDT)
- AMBER: problem with editing with xleap moitrayee.mbu.iisc.ernet.in (Tue Sep 16 2008 - 08:50:38 PDT)
- AMBER: AMBER9 Compilation chen bents (Tue Sep 16 2008 - 18:25:59 PDT)
- AMBER: amber 9 install chen bents (Tue Sep 16 2008 - 20:14:47 PDT)
- AMBER: acetone box parvesh singh (Wed Sep 17 2008 - 04:09:01 PDT)
- AMBER: Question Beale, John (Wed Sep 17 2008 - 04:14:15 PDT)
- AMBER: MD simulation crashed Aust, Susanne (Wed Sep 17 2008 - 06:10:17 PDT)
- AMBER: adding new potential function Harianto Tjong (Wed Sep 17 2008 - 12:12:34 PDT)
- AMBER: Some Problems With the Installation of Ambertools Manikandan Chandrasekaran (Wed Sep 17 2008 - 16:21:06 PDT)
- AMBER: Dihedral: ptraj waqasuddin.khan.iccs.edu (Wed Sep 17 2008 - 23:39:33 PDT)
- AMBER: Single point energy calculations with explicit solvent. Waqas Nasir (Thu Sep 18 2008 - 05:48:47 PDT)
- AMBER: problem with traj and strip waters Steve Seibold (Thu Sep 18 2008 - 06:08:21 PDT)
- AMBER: problem with traj and strip waters Steve Seibold (Thu Sep 18 2008 - 07:13:38 PDT)
- AMBER: Error: PB bomb in pb_reslist(): maxnbr too small Rajendra P. OJHA (Thu Sep 18 2008 - 07:34:15 PDT)
- AMBER: RMSD restraint in umbrella sampling nurith.rice.edu (Thu Sep 18 2008 - 13:36:24 PDT)
- AMBER: help can amber couple part of the system to different heat bath? Jose Borreguero (Thu Sep 18 2008 - 14:09:23 PDT)
- AMBER: help can amber couple part of the system to different heat bath? Jose Borreguero (Thu Sep 18 2008 - 14:09:27 PDT)
- AMBER: problems with ptraj and strip waters Steve Seibold (Thu Sep 18 2008 - 14:19:25 PDT)
- AMBER: increasing temperature smoothly Germain Vallverdu (Fri Sep 19 2008 - 08:17:56 PDT)
- AMBER: molecule drift out of water box? Qiuting Hong (Fri Sep 19 2008 - 16:39:42 PDT)
- AMBER: Dihedral Drive Hashem Taha (Sat Sep 20 2008 - 00:31:13 PDT)
- Re: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? cgji (Sat Sep 20 2008 - 09:22:07 PDT)
- AMBER: Is there any way I can extract the potential energy of the solute with the solvent instead of the total energy in Amber? Zhao, Zhen (zhaozh) (Sat Sep 20 2008 - 13:01:59 PDT)
- AMBER: bis(trifluoromethylsulfonyl)imide (Tf2N) babak minoofar (Sun Sep 21 2008 - 07:34:39 PDT)
- AMBER: multiple heat baths in a single simulation? Jose Borreguero (Sun Sep 21 2008 - 16:09:41 PDT)
- AMBER: fix for POL3 heating problem? Grange Hermitage (Mon Sep 22 2008 - 02:35:02 PDT)
- AMBER: Re: reaction coordinate in umbrella sampling Sudha Mani Karra (Mon Sep 22 2008 - 08:00:42 PDT)
- AMBER: Position: Postdoctoral Fellow Willy Valdivia-Granda (Mon Sep 22 2008 - 08:50:48 PDT)
- AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba. Zhao, Zhen (zhaozh) (Mon Sep 22 2008 - 12:02:27 PDT)
- AMBER: MMPBSA error Cristina Sisu (Tue Sep 23 2008 - 03:30:38 PDT)
- AMBER: replica exchange with amber9 greddy1.umd.edu (Tue Sep 23 2008 - 15:44:24 PDT)
- AMBER: MD goes wrong baohua zhang (Tue Sep 23 2008 - 19:17:57 PDT)
- AMBER: to prepare pdb file fro unusual amino acid. priya priya (Wed Sep 24 2008 - 01:03:06 PDT)
- AMBER: error while running REMD in amber9 priya priya (Wed Sep 24 2008 - 10:53:09 PDT)
- AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support Pablo Englebienne (Wed Sep 24 2008 - 12:04:46 PDT)
- AMBER: solvate without translating Anuradha Mittal (Wed Sep 24 2008 - 12:38:31 PDT)
- AMBER: how to enlarge the TIP3PBOX size Qiuting Hong (Wed Sep 24 2008 - 15:56:10 PDT)
- AMBER: Amber GB problems on PMEMD !! Sampath Koppole (Thu Sep 25 2008 - 02:09:30 PDT)
- AMBER: Problem In Paralklel Amber Ranga Swamy (Fri Sep 26 2008 - 04:10:13 PDT)
- AMBER: MD at a given pH Beale, John (Fri Sep 26 2008 - 09:44:32 PDT)
- AMBER: Harmonic restraint between two atoms greddy1.umd.edu (Fri Sep 26 2008 - 11:37:34 PDT)
- Re: AMBER: MM_PBSA snapshot statistic calc problem haixiao jin (Fri Sep 26 2008 - 23:40:20 PDT)
- AMBER: mmpbsa errors in redoing the tutorial A3:MMPBSA haixiao jin (Sat Sep 27 2008 - 00:45:06 PDT)
- AMBER: Constant pH simulation force field Soonmin Jang (Sat Sep 27 2008 - 02:13:51 PDT)
- AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Sat Sep 27 2008 - 06:46:10 PDT)
- AMBER: a question Adrien Delmont (Sun Sep 28 2008 - 15:08:00 PDT)
- AMBER: energy terms in hybrid REMD calculation Ye Mei (Mon Sep 29 2008 - 02:28:13 PDT)
- AMBER: Location of vdw radii and partial charges for ff99SB Charles Letner, Ph.D. (Mon Sep 29 2008 - 06:08:27 PDT)
- AMBER: unsubscribe amber steinbrt.scripps.edu (Mon Sep 29 2008 - 07:57:50 PDT)
- AMBER: coordinate file question Robert Hanson (Mon Sep 29 2008 - 20:16:25 PDT)
- AMBER: Ac-Co Parameters for Amber suhaib sh (Tue Sep 30 2008 - 04:49:41 PDT)
- AMBER: Ca ions not recognized Cristina Sisu (Tue Sep 30 2008 - 07:00:24 PDT)
- AMBER: Buckingham potential Diddo Diddens (Tue Sep 30 2008 - 07:16:47 PDT)
- AMBER: cluster for running amber10 Guillermo Mulliert Carlín (Tue Sep 30 2008 - 08:14:07 PDT)
- AMBER: problem with parmchck aneesh cna (Tue Sep 30 2008 - 10:10:28 PDT)
- AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE liu junjun (Tue Sep 30 2008 - 11:07:09 PDT)
- AMBER: FW: Amber 9 mhamed.birzeit.edu (Tue Sep 30 2008 - 10:22:07 PDT)
- AMBER: problem of use MPICHI2 to run RMED on amber10 xwu.purdue.edu (Tue Sep 30 2008 - 13:31:24 PDT)
- AMBER: How to set up a water slab in Amber? Zhao, Zhen (zhaozh) (Tue Sep 30 2008 - 14:23:06 PDT)
- Last message date: Wed Oct 01 2008 - 05:12:12 PDT
- Archived on: Fri Apr 19 2024 - 05:53:28 PDT
