Amber Archive Nov 2006 by thread
- AMBER: Mass weights Sergey Samsonov (Wed Nov 01 2006 - 00:41:33 PST)
- Re: AMBER: Closest(closest water) Sergey Samsonov (Wed Nov 01 2006 - 00:38:55 PST)
- AMBER: How to start a Simulation of a peptide in bilayer nur avneet (Wed Nov 01 2006 - 01:28:31 PST)
- AMBER: ab initio terminology query HL Eastwood (Wed Nov 01 2006 - 03:38:24 PST)
- AMBER: PCA and projections Miguel Ferreira (Wed Nov 01 2006 - 06:11:57 PST)
- AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Yu Chen (Wed Nov 01 2006 - 08:22:54 PST)
- AMBER: grid output Sergey Samsonov (Wed Nov 01 2006 - 08:31:34 PST)
- AMBER: GBSA implicit chloroform nadiav.soton.ac.uk (Wed Nov 01 2006 - 08:41:18 PST)
- AMBER: NEWPDB.PDB from antechamber Esther Brugger (Wed Nov 01 2006 - 08:59:29 PST)
- AMBER: too big EEL values in the minimisation output Rachel (Wed Nov 01 2006 - 09:01:17 PST)
- Re: AMBER: mm_pbsa does not terminate Holly Freedman (Wed Nov 01 2006 - 09:56:28 PST)
- AMBER: Problem of QM/MM calculation with amber 9 parallel version Lee Kyung-koo (Wed Nov 01 2006 - 11:50:28 PST)
- AMBER: How the ensemble average calculated in Gibbs, AMBER7? Yongmei Pan (Wed Nov 01 2006 - 14:06:09 PST)
- [RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Lee Kyung-koo (Wed Nov 01 2006 - 15:25:25 PST)
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth (Wed Nov 01 2006 - 22:48:03 PST)
- [RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Lee Kyung-koo (Thu Nov 02 2006 - 00:53:53 PST)
- AMBER: leap usage Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu Nov 02 2006 - 01:41:34 PST)
- AMBER: Interaction Energy Calculation Varsha Goyal (Thu Nov 02 2006 - 13:34:28 PST)
- AMBER: ntt=1 in simulated annealing Tanya Johannsen (Thu Nov 02 2006 - 19:44:19 PST)
- AMBER: how to choose the parameter for the production/sampling run after the equilibration run hbluo (Fri Nov 03 2006 - 17:57:01 PST)
- AMBER: Problems with equilibrating the starting density Markus Weingarth (Fri Nov 03 2006 - 09:32:20 PST)
- AMBER: pmemd installation problem Ed Pate (Fri Nov 03 2006 - 10:51:36 PST)
- AMBER: Re: Fluorine and Bromine Parameters in Amber 9 Philip Cheung (Fri Nov 03 2006 - 11:56:52 PST)
- AMBER: I got the error meassage in testcase of QMMM Lee Kyung-koo (Fri Nov 03 2006 - 21:33:44 PST)
- AMBER: PTRAJ RMS: dumping RMSd vs time data r. a. (Sat Nov 04 2006 - 00:45:25 PST)
- AMBER: PTRAJ RMS: dumping RMSd vs time data r. a. (Sat Nov 04 2006 - 00:58:25 PST)
- AMBER: Unable to find solution for an error - "cannot successfully assign bond type" Rama krishnan (Sat Nov 04 2006 - 02:06:51 PST)
- AMBER: Ross Walker (Sat Nov 04 2006 - 09:35:43 PST)
- AMBER: RE: I got the error meassage in testcase of QMMM Ross Walker (Sat Nov 04 2006 - 10:09:13 PST)
- AMBER: ACS Chicago potential symposia and OASYS abstracts Thomas Cheatham (Sat Nov 04 2006 - 13:04:47 PST)
- AMBER: Combine amber-force field and gaff94 for one molecule? Michel Becker (Sun Nov 05 2006 - 09:45:05 PST)
- AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Margaret S. Cheung (Sun Nov 05 2006 - 15:16:34 PST)
- AMBER: Mutual exclusion of atoms Nitin Bhardwaj (Sun Nov 05 2006 - 21:59:38 PST)
- AMBER: Potential Energy Calculation sangeeta (Mon Nov 06 2006 - 04:11:30 PST)
- AMBER: problem with NAD+ parameters Urszula Uciechowska (Mon Nov 06 2006 - 06:27:16 PST)
- AMBER: top2mol2.c scanf format string bug Chris Moth (Mon Nov 06 2006 - 16:19:36 PST)
- AMBER: klambda for TI method. Biswa Ranjan Meher (Tue Nov 07 2006 - 04:59:15 PST)
- [RE]AMBER: RE: I got the error meassage in testcase of QMMM Lee Kyung-koo (Tue Nov 07 2006 - 08:46:25 PST)
- AMBER: building a box kepa koldo burusco (Tue Nov 07 2006 - 08:52:28 PST)
- [RE]AMBER: RE: I got the error meassage in testcase of QMMM Lee Kyung-koo (Tue Nov 07 2006 - 08:59:16 PST)
- AMBER: error about the number of snapshots AYTUG TUNCEL (Tue Nov 07 2006 - 13:11:24 PST)
- AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST) Nitin Bhardwaj (Tue Nov 07 2006 - 13:08:42 PST)
- AMBER: Atom Exclusion Nitin Bhardwaj (Tue Nov 07 2006 - 21:44:30 PST)
- AMBER: Re: Unit of force Kakali Sen (Tue Nov 07 2006 - 22:41:30 PST)
- AMBER: question about the topology file J. Zhang (Wed Nov 08 2006 - 01:24:10 PST)
- AMBER: Unit of force Kakali Sen (Wed Nov 08 2006 - 03:06:16 PST)
- AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Wed Nov 08 2006 - 04:59:00 PST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity David A. Case (Wed Nov 08 2006 - 08:48:01 PST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Wed Nov 08 2006 - 09:31:12 PST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Carlos Simmerling (Wed Nov 08 2006 - 09:46:27 PST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity David A. Case (Wed Nov 08 2006 - 13:35:10 PST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Fri Nov 10 2006 - 06:42:31 PST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Carlos Simmerling (Fri Nov 10 2006 - 06:58:26 PST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Fri Nov 10 2006 - 07:54:26 PST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity David A. Case (Fri Nov 10 2006 - 08:34:45 PST)
- RE: AMBER: vlimit exceeded for step 0, vmax = infinity Yong Duan (Fri Nov 10 2006 - 13:55:23 PST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Mon Nov 13 2006 - 09:09:22 PST)
- RE: AMBER: vlimit exceeded for step 0, vmax = infinity Yong Duan (Mon Nov 13 2006 - 17:56:29 PST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Tue Nov 14 2006 - 14:44:44 PST)
- RE: AMBER: vlimit exceeded for step 0, vmax = infinity Yong Duan (Tue Nov 14 2006 - 15:05:08 PST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Carlos Simmerling (Wed Nov 08 2006 - 10:35:21 PST)
- AMBER: NAD ?? Urszula Uciechowska (Wed Nov 08 2006 - 05:40:15 PST)
- AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion Rajesh Murarka (Wed Nov 08 2006 - 07:59:36 PST)
- AMBER: simulating a small chain protein in water box Dave, Sonya (Wed Nov 08 2006 - 08:03:46 PST)
- AMBER: Problems amber mask in distance? Sergey Samsonov (Wed Nov 08 2006 - 08:39:18 PST)
- AMBER: big bond energy change from minimization and md (heating) Rachel (Wed Nov 08 2006 - 08:40:12 PST)
- AMBER: problem in calculating EGB using sander for ligand containing F atom VANDANA KUMARI (Wed Nov 08 2006 - 19:36:52 PST)
- AMBER: Amber H-bond print? Andres Palencia (Thu Nov 09 2006 - 01:07:46 PST)
- AMBER: Probelm with running Amber 9 parallelly Rafi Ahmad (Thu Nov 09 2006 - 04:59:56 PST)
- AMBER: Building Library Steve Seibold (Thu Nov 09 2006 - 08:52:08 PST)
- AMBER: Steve Seibold (Thu Nov 09 2006 - 09:03:14 PST)
- AMBER: antechamber:tutorial Lwin, ThuZar (Thu Nov 09 2006 - 10:48:58 PST)
- AMBER: FW: antechamber:tutorial Lwin, ThuZar (Thu Nov 09 2006 - 11:03:46 PST)
- AMBER: Building Library Steve Seibold (Thu Nov 09 2006 - 11:40:30 PST)
- AMBER: strange temperature behavior when changing to constant pressure Joshua (Thu Nov 09 2006 - 11:52:33 PST)
- RE: AMBER: antechamber:tutorial. . Lwin, ThuZar (Thu Nov 09 2006 - 12:02:28 PST)
- AMBER: sander error: rst file crash jitrayut jitonnom (Fri Nov 10 2006 - 04:52:19 PST)
- AMBER: PTRAJ: radius of gyration kepa koldo burusco (Fri Nov 10 2006 - 09:05:09 PST)
- Re: AMBER: PTRAJ: radius of gyration Bill Ross (Fri Nov 10 2006 - 11:04:06 PST)
- AMBER: <kein Betreff> Michel Becker (Mon Nov 13 2006 - 03:21:58 PST)
- AMBER: what to do with the counter ions when minimizing average structure of DNA? Chengwen Chen (Tue Nov 14 2006 - 03:09:25 PST)
- AMBER: how to remove the rotation of system in periodic condition? 张勇 (Tue Nov 14 2006 - 04:10:22 PST)
- AMBER: gfortran/gcc versus ifort/icc Lachele Foley (Lists) (Tue Nov 14 2006 - 06:35:21 PST)
- AMBER: Ptraj: radial distribution and correlation coefficient Austin B. Yongye (Tue Nov 14 2006 - 10:10:39 PST)
- AMBER: Acetone box SERGIO MIGUEL FERNANDES DOS SANTOS (Tue Nov 14 2006 - 10:34:24 PST)
- AMBER: Restraints of the strand-endings? Michel Becker (Tue Nov 14 2006 - 12:22:36 PST)
- Re: AMBER: Restraints of the strand-endings? Bill Ross (Tue Nov 14 2006 - 14:19:06 PST)
- AMBER: error in tleap test Christian Roth (Tue Nov 14 2006 - 16:40:24 PST)
- AMBER: ptraj and mdvel question Jianhui (Wed Nov 15 2006 - 11:07:06 PST)
- AMBER: H-Bond Terms in amber force field Ilyas Yildirim (Wed Nov 15 2006 - 11:28:06 PST)
- AMBER: Error in compliling LEAP on Fedora 5 Pankaj Daga (Wed Nov 15 2006 - 14:56:58 PST)
- AMBER: MM_PBSA Varsha Goyal (Wed Nov 15 2006 - 18:27:15 PST)
- AMBER: erroneous placement of TER card Gregory Sandala (Thu Nov 16 2006 - 01:12:43 PST)
- AMBER: opls_aa in amber Vitor Manuel Sousa F?x (Thu Nov 16 2006 - 06:29:45 PST)
- AMBER: pqr file Seth Lilavivat (Thu Nov 16 2006 - 08:43:55 PST)
- AMBER: GLYCAM and ff98 atom-types Gabbar S. Daaku (Thu Nov 16 2006 - 10:11:05 PST)
- AMBER: Xleap woes Shozeb Haider (Thu Nov 16 2006 - 15:07:01 PST)
- AMBER: parameters for beta peptides yipinl.umich.edu (Thu Nov 16 2006 - 11:29:08 PST)
- Re: AMBER: GLYCAM and ff98 atom-types] Austin B. Yongye (Thu Nov 16 2006 - 11:53:03 PST)
- AMBER: optimatized structure is so much different from the original pdb structure emilia wu (Thu Nov 16 2006 - 21:38:18 PST)
- AMBER: Ethanol Rita Cassia (Fri Nov 17 2006 - 04:13:14 PST)
- AMBER: dihedral angle equation Vitor Manuel Sousa F?x (Fri Nov 17 2006 - 04:41:25 PST)
- AMBER: gfortran and amber9 success on FreeBSD M. L. Dodson (Sat Nov 18 2006 - 14:02:16 PST)
- AMBER: parameters for silicon atom Chengwen Chen (Sun Nov 19 2006 - 23:45:07 PST)
- AMBER: problems with saving self-built molecules parameters Rachel (Mon Nov 20 2006 - 04:59:07 PST)
- AMBER: Combining Residues in LEaP for Lipid Bilayers Matthew Tessier (Mon Nov 20 2006 - 09:09:13 PST)
- AMBER: the energy and temperature both increasing during the simulation with NTT=0 Xiaowei (David) Li (Mon Nov 20 2006 - 10:50:00 PST)
- AMBER: matrix correl Jardas sucuriba (Tue Nov 21 2006 - 05:05:41 PST)
- AMBER: Quantifying pi-pi interactions zachary hartman (Tue Nov 21 2006 - 07:51:30 PST)
- AMBER: ff03 GLY HAs atom type Sandro Fornili (Tue Nov 21 2006 - 08:21:01 PST)
- AMBER: compile amber8 on IBM-sp4 Rachel (Tue Nov 21 2006 - 09:56:13 PST)
- AMBER: Ptraj: diffusion rate Austin B. Yongye (Tue Nov 21 2006 - 13:03:52 PST)
- AMBER: Ptraj: correlation time Austin B. Yongye (Tue Nov 21 2006 - 13:05:52 PST)
- AMBER: Some warning !!! during SANDER ? jitrayut jitonnom (Wed Nov 22 2006 - 00:20:36 PST)
- AMBER: Ptraj syntax change Amber8->Amber9 ? Markus Kaukonen (Wed Nov 22 2006 - 02:35:26 PST)
- AMBER: Radius of gyration r. a. (Wed Nov 22 2006 - 02:11:14 PST)
- AMBER: SHAKE problem after minimization Rachel (Wed Nov 22 2006 - 03:39:18 PST)
- AMBER: Problem with mask when using distance in ptraj Christopher Gaughan (Wed Nov 22 2006 - 11:36:23 PST)
- AMBER: ammonia parameters Peter Trodler (Thu Nov 23 2006 - 00:51:39 PST)
- AMBER: Restarting with new topology Sergey Samsonov (Thu Nov 23 2006 - 08:39:53 PST)
- AMBER: Snapshots (pdbs) from a trajectory. Jordi Rodrigo De Losada (Thu Nov 23 2006 - 09:11:18 PST)
- AMBER: Unable to find mopac charges in divcon.out Rachel (Thu Nov 23 2006 - 11:31:55 PST)
- AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines Rachel (Fri Nov 24 2006 - 09:58:53 PST)
- AMBER: Antechamber and gaussian questions Fenghui Fan (Fri Nov 24 2006 - 14:04:40 PST)
- AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64 In Hee Park (Fri Nov 24 2006 - 14:50:54 PST)
- AMBER: bondtype problem Fenghui Fan (Fri Nov 24 2006 - 16:22:23 PST)
- AMBER: respin file Fenghui Fan (Fri Nov 24 2006 - 23:06:49 PST)
- AMBER: resp Fenghui Fan (Sat Nov 25 2006 - 13:03:00 PST)
- AMBER: respin file Fenghui Fan (Sat Nov 25 2006 - 14:23:46 PST)
- AMBER: how can i treat with long "mask" in ptraj analysis. Changge Ji (Sun Nov 26 2006 - 08:22:00 PST)
- AMBER: ZN prepin Fenghui Fan (Sun Nov 26 2006 - 14:29:31 PST)
- AMBER: bond information Fenghui Fan (Sun Nov 26 2006 - 20:10:42 PST)
- AMBER: ptraj grid Hannes Loeffler (Sun Nov 26 2006 - 20:05:05 PST)
- AMBER: helices in GB simulations Marie-Pierre Durrieu (Mon Nov 27 2006 - 09:43:41 PST)
- AMBER: minimization of Hydrogens with xLeaP rebeca.mmb.pcb.ub.es (Mon Nov 27 2006 - 10:38:04 PST)
- AMBER: Problem Installing Amber in SGI Irix 6.5 trudy.uoguelph.ca (Mon Nov 27 2006 - 12:29:53 PST)
- AMBER: phantom sander8 in dmesg Lachele Foley (Lists) (Mon Nov 27 2006 - 13:25:57 PST)
- AMBER: prepin file nan Fenghui Fan (Mon Nov 27 2006 - 19:28:16 PST)
- AMBER: Problem about dummy atoms when running antechamber 한 민우 (Mon Nov 27 2006 - 19:30:27 PST)
- AMBER: protonated phosphate Einar Uggerud (Mon Nov 27 2006 - 23:11:46 PST)
- AMBER: NONB values adjusted? Dave S Walker (Mon Nov 27 2006 - 23:37:28 PST)
- AMBER: energy minimizations in amber8 vs. amber9 Seongeun Yang (Mon Nov 27 2006 - 23:43:35 PST)
- AMBER: How to specify user defined force fields or its parameters in amber?? Gobind Singh Bisht (Tue Nov 28 2006 - 03:51:30 PST)
- AMBER: xleap Steve Seibold (Tue Nov 28 2006 - 06:33:48 PST)
- AMBER: uccadco.ucl.ac.uk (Tue Nov 28 2006 - 06:48:08 PST)
- AMBER: Modifying a Force Field Seth Lilavivat (Tue Nov 28 2006 - 07:27:08 PST)
- AMBER: nmode output with ptraj nadiav.soton.ac.uk (Tue Nov 28 2006 - 07:59:02 PST)
- AMBER: Charge fitting in Amber Changge Ji (Tue Nov 28 2006 - 08:50:20 PST)
- AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 Michael John Hanby (Tue Nov 28 2006 - 10:06:16 PST)
- AMBER: ambpdb -pqr Seth Lilavivat (Tue Nov 28 2006 - 12:52:10 PST)
- AMBER: RE: Amber: ZN-complex file Junmei Wang (Tue Nov 28 2006 - 15:21:40 PST)
- AMBER: Periodic simulations with net charge Jennie Thomas (Tue Nov 28 2006 - 16:47:32 PST)
- AMBER: How to apply a force to some atom in a residues? a a (Tue Nov 28 2006 - 19:36:15 PST)
- AMBER: Solvation Energies Ivelin Georgiev (Wed Nov 29 2006 - 06:31:13 PST)
- AMBER: Confusion about PBC anna.schrey.gmx.de (Wed Nov 29 2006 - 08:26:04 PST)
- AMBER: Langevin temperature control vs berendson heat bath Hayden Eastwood (Wed Nov 29 2006 - 10:12:16 PST)
- AMBER: ptraj----radial output files Esther Brugger (Wed Nov 29 2006 - 12:03:20 PST)
- AMBER: How to run MD simulation of a silicon containing complex with AMBER9? Chengwen Chen (Wed Nov 29 2006 - 23:06:54 PST)
- AMBER: How to specify a box with few walls rigid and others with periodic boundary conditions and then apply a pressure gradient across it? Gobind Singh Bisht (Wed Nov 29 2006 - 23:34:28 PST)
- AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes Chengwen Chen (Thu Nov 30 2006 - 00:07:28 PST)
- AMBER: Performing Interactive Essential Dynamics in Ptraj hbluo (Thu Nov 30 2006 - 16:58:11 PST)
- AMBER: amber9 parralel compiling Nikola Trbovic (Thu Nov 30 2006 - 08:31:22 PST)
- AMBER: How to recompile sander for single-processor use in AMBER 8? Peter Anderson (Thu Nov 30 2006 - 13:41:27 PST)
- AMBER: watershell and image commands Esther Brugger (Thu Nov 30 2006 - 14:37:58 PST)
- AMBER: watershell command Esther Brugger (Thu Nov 30 2006 - 15:16:52 PST)
- AMBER: H-bond analysis (Ptraj) Esther Brugger (Thu Nov 30 2006 - 17:28:10 PST)
- Last message date: Sun Dec 03 2006 - 06:07:40 PST
- Archived on: Mon Dec 23 2024 - 05:53:29 PST
