Amber Archive Aug 2007 by thread
- AMBER: how to calculate the ps/day of md simulation using using my cluster system in amber7 Syed Tarique Moin (Wed Aug 01 2007 - 02:36:31 PDT)
- AMBER: problem compiling Amber9 on 64-machine fatima.chami.durham.ac.uk (Wed Aug 01 2007 - 04:03:48 PDT)
- Fwd: RE: AMBER: Average potential energies and conformer ratios Francesco Pietra (Wed Aug 01 2007 - 06:58:02 PDT)
- AMBER: Problem with Antechamber and point charges anna duraj (Wed Aug 01 2007 - 12:40:44 PDT)
- AMBER: neutral terminals Jena M (Wed Aug 01 2007 - 17:15:46 PDT)
- Re: AMBER: bugfix for impropers in parmchk Jiten (Wed Aug 01 2007 - 21:02:24 PDT)
- Re: AMBER: Problem while saving .top and .crd files. Anju Sharma (Wed Aug 01 2007 - 22:25:19 PDT)
- AMBER: Problem with antechamber Anju Sharma (Wed Aug 01 2007 - 23:34:39 PDT)
- AMBER: (no subject) Syed Tarique Moin (Wed Aug 01 2007 - 23:50:59 PDT)
- AMBER: planarity restraints for NA Seth Lilavivat (Thu Aug 02 2007 - 06:12:18 PDT)
- AMBER: restrained md and mm pbsa Christopher Gaughan (Thu Aug 02 2007 - 07:15:17 PDT)
- AMBER: vector corrplane Servaas Michielssens (Thu Aug 02 2007 - 08:25:45 PDT)
- AMBER: Force Field Parameters Beale, John (Thu Aug 02 2007 - 09:46:16 PDT)
- AMBER: Calculating cumulative average Francesco Pietra (Thu Aug 02 2007 - 10:00:10 PDT)
- AMBER: edit.out amber version 9 Greg Gannon (Thu Aug 02 2007 - 11:21:31 PDT)
- AMBER: Problem generating .prepin file in Antechamber Lili Peng (Thu Aug 02 2007 - 12:07:11 PDT)
- AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Thu Aug 02 2007 - 17:33:40 PDT)
- Re: AMBER: Antechamber formal charges with Gasteiger method Scott Brozell (Thu Aug 02 2007 - 18:44:28 PDT)
- AMBER: Information about Amber 9 Lycourgos Chiniadis (Thu Aug 02 2007 - 22:11:17 PDT)
- AMBER: force field for hydrogels Prem Prakash Pathak (Thu Aug 02 2007 - 23:03:48 PDT)
- AMBER: unable to save prmtop/inpcrd for chcl3box Francesco Pietra (Fri Aug 03 2007 - 03:09:03 PDT)
- AMBER: Fwd: unable to save prmtop/inpcrd for chcl3box Francesco Pietra (Fri Aug 03 2007 - 05:24:24 PDT)
- AMBER: Successful compile on Mac OSX + Intel compilers Viv Kendon (Fri Aug 03 2007 - 05:28:56 PDT)
- Re: AMBER: bug in nonbond_list.f (nee ew_setup.f) David A. Case (Fri Aug 03 2007 - 08:14:27 PDT)
- AMBER: Binary file curiosities David LeBard (Fri Aug 03 2007 - 15:59:45 PDT)
- AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sat Aug 04 2007 - 01:32:40 PDT)
- AMBER: nucleic acid electrostatic energy Tiago Sobreira (Sat Aug 04 2007 - 06:45:46 PDT)
- AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sat Aug 04 2007 - 07:33:35 PDT)
- AMBER: GAFF atom typing for flavin Hans Martin Senn (Sat Aug 04 2007 - 09:15:30 PDT)
- AMBER: force field for irregulate DNA ends Hu, Shaowen (JSC-SK)[USRA] (Sat Aug 04 2007 - 11:20:42 PDT)
- AMBER: setting dimensions of truncated octahedron Lillian chong (Sat Aug 04 2007 - 13:34:59 PDT)
- AMBER: RE: tutorial file polyAT_vac.prmtop Ross Walker (Sun Aug 05 2007 - 20:09:46 PDT)
- AMBER: Problem while carrying out minimisation of drug molecule using sander Anju Sharma (Sun Aug 05 2007 - 20:51:11 PDT)
- AMBER: Specific heat graph is a straight line priya priya (Mon Aug 06 2007 - 06:33:52 PDT)
- AMBER: Integrating the alpha-helix bias correction into ff94 Andrew Borgert (Mon Aug 06 2007 - 12:18:58 PDT)
- AMBER: hybridization in Amber, pertaining to resonant structures, ions Karen Callahan (Mon Aug 06 2007 - 21:13:27 PDT)
- AMBER: heical content in simulations priya priya (Tue Aug 07 2007 - 00:58:12 PDT)
- AMBER: Problem with minimization Syed Tarique Moin (Tue Aug 07 2007 - 06:11:32 PDT)
- AMBER: compile amber8 with mpich2 Kailee (Tue Aug 07 2007 - 06:18:14 PDT)
- AMBER: Positive EPtot in QM-MM Francesco Pietra (Tue Aug 07 2007 - 07:34:35 PDT)
- AMBER: about shake linfu (Tue Aug 07 2007 - 18:36:59 PDT)
- AMBER: msubhamoy.ibab.ac.in (Wed Aug 08 2007 - 06:01:00 PDT)
- AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA msubhamoy.ibab.ac.in (Wed Aug 08 2007 - 06:08:04 PDT)
- AMBER: RE: TUTORIAL B1 file polyAT_vac.prmtop Ross Walker (Wed Aug 08 2007 - 07:52:39 PDT)
- AMBER: RE: Problem loading pdf into tleap Ross Walker (Wed Aug 08 2007 - 10:29:19 PDT)
- AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 14:33:22 PDT)
- Re: AMBER: Cygwin error Bill Ross (Wed Aug 08 2007 - 14:43:49 PDT)
- Re: AMBER: program bug? M. Maeda (Wed Aug 08 2007 - 19:37:13 PDT)
- AMBER: how to combine two molecules Wenyong Tong (Wed Aug 08 2007 - 22:34:33 PDT)
- AMBER: NVE energy and temperature drift Nikola Trbovic (Thu Aug 09 2007 - 13:24:11 PDT)
- AMBER: Implicit solvent simulation is too slow. SeungPyo Hong (Fri Aug 10 2007 - 05:42:11 PDT)
- AMBER: How to couple only one residue to the temperature bath? Michael Lerner (Fri Aug 10 2007 - 07:45:10 PDT)
- AMBER: short 2'OH-OP contacts in RNA Jose Gallego (Fri Aug 10 2007 - 09:22:35 PDT)
- AMBER: vlimit exceeded for the step Sudha Mani Karra (Fri Aug 10 2007 - 12:31:08 PDT)
- AMBER: Steve Seibold (Fri Aug 10 2007 - 13:17:47 PDT)
- AMBER: Citation for Langevin thermostat? Marc Baaden (Sat Aug 11 2007 - 00:13:28 PDT)
- AMBER: Using charmm force field in amber Seongeun Yang (Sat Aug 11 2007 - 01:44:44 PDT)
- AMBER: Failure to SCF convergence Francesco Pietra (Sat Aug 11 2007 - 09:56:53 PDT)
- AMBER: imin=5 and inptraj Nikola Trbovic (Sat Aug 11 2007 - 13:11:08 PDT)
- AMBER: Neutralize charges for simulated annealing? Francesco Pietra (Sat Aug 11 2007 - 15:35:30 PDT)
- AMBER: setbox command error priya priya (Mon Aug 13 2007 - 09:18:16 PDT)
- AMBER: unsubscribe Pan, Yongmei (Mon Aug 13 2007 - 10:35:12 PDT)
- AMBER: Using TLEAP to set up MD in the crystal lattice space? David Cerutti (Mon Aug 13 2007 - 14:09:51 PDT)
- AMBER: Normal Mode Analysis Kresimir Sikic (Mon Aug 13 2007 - 08:12:59 PDT)
- AMBER: Machine environment to install AMBER 8 M. Maeda (Mon Aug 13 2007 - 23:03:07 PDT)
- AMBER: regarding implicit simulation gurpreet singh (Mon Aug 13 2007 - 23:21:35 PDT)
- AMBER: MMPBSA NOT Getting results msubhamoy.ibab.ac.in (Tue Aug 14 2007 - 01:26:57 PDT)
- AMBER: How to carry out drug-dna complex simulations Anju Sharma (Tue Aug 14 2007 - 01:50:04 PDT)
- AMBER: Tutorial about SMD? Qiang Zhong (Tue Aug 14 2007 - 03:19:09 PDT)
- AMBER: Parallelizin antechamber? Francesco Pietra (Tue Aug 14 2007 - 06:29:11 PDT)
- AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 13:31:34 PDT)
- AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 01:43:45 PDT)
- AMBER: Building parallel Amber 9.0 Beale, John (Wed Aug 15 2007 - 05:21:56 PDT)
- AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra (Wed Aug 15 2007 - 07:38:06 PDT)
- AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade (Wed Aug 15 2007 - 09:50:57 PDT)
- AMBER: docking ability anna duraj (Wed Aug 15 2007 - 10:34:37 PDT)
- AMBER: Bug in ptraj mask processing? Steve Spronk (Wed Aug 15 2007 - 12:18:15 PDT)
- AMBER: Missplaced TERs Steve Seibold (Thu Aug 16 2007 - 11:35:26 PDT)
- AMBER: What is the best computer for running AMBER simulations? Lili Peng (Thu Aug 16 2007 - 14:37:03 PDT)
- Re: AMBER: MPI Quiescence problem in REMD In Hee Park (Thu Aug 16 2007 - 15:56:37 PDT)
- AMBER: NAN and vlimit exceeded errors in restrained MD.. using IBELLY Sandeep Kaushik (Thu Aug 16 2007 - 22:44:17 PDT)
- AMBER: Thermodynamic Integration for a CHARGED molecule ming hui (Fri Aug 17 2007 - 02:12:38 PDT)
- AMBER: MPI Beale, John (Fri Aug 17 2007 - 05:00:33 PDT)
- AMBER: Molsurf error Pankaj R. Daga (Fri Aug 17 2007 - 10:46:54 PDT)
- AMBER: ptraj hydrogen bonding defaults Michael Lerner (Fri Aug 17 2007 - 15:26:09 PDT)
- AMBER: DFTB email address Francesco Pietra (Sat Aug 18 2007 - 00:14:53 PDT)
- AMBER: charges in PBSA calculation Neha Gandhi (Sat Aug 18 2007 - 19:20:16 PDT)
- AMBER: CRESP charges in antechamber prepin Francesco Pietra (Mon Aug 20 2007 - 00:23:24 PDT)
- AMBER: mmpbsa calculation msubhamoy.ibab.ac.in (Mon Aug 20 2007 - 02:53:42 PDT)
- AMBER: TEST_FAILURES Qiang Zhong (Mon Aug 20 2007 - 05:59:28 PDT)
- AMBER: Entropy in MM_PBSA Sergey Samsonov (Mon Aug 20 2007 - 08:01:37 PDT)
- AMBER: Beale, John (Mon Aug 20 2007 - 08:41:06 PDT)
- AMBER: $tleap is not normal Qiang Zhong (Mon Aug 20 2007 - 18:34:00 PDT)
- AMBER: Regarding free energy calculation and covalent bond nag raj (Mon Aug 20 2007 - 21:07:04 PDT)
- AMBER: Error in MMPBSA Calculation msubhamoy.ibab.ac.in (Mon Aug 20 2007 - 22:53:17 PDT)
- AMBER: command tleap is not normal Qiang Zhong (Tue Aug 21 2007 - 01:12:44 PDT)
- AMBER: how to include mpirun in this script Syed Tarique Moin (Tue Aug 21 2007 - 03:50:12 PDT)
- AMBER: How to use AMBER Parameter Database ? Qiang Zhong (Tue Aug 21 2007 - 05:36:46 PDT)
- AMBER: Thermodynamic Integration for conformational changes? Francesco Pietra (Tue Aug 21 2007 - 09:57:47 PDT)
- AMBER: xLeap "Could not find type" error Lili Peng (Tue Aug 21 2007 - 12:28:46 PDT)
- AMBER: Octahedral box orientation David Cerutti (Tue Aug 21 2007 - 06:08:38 PDT)
- AMBER: Force field for RNA with U-turn motif Cenk Andac (Tue Aug 21 2007 - 06:52:48 PDT)
- AMBER: Tutorial of document about QM/MM in reaction pathways? Qiang Zhong (Tue Aug 21 2007 - 07:06:53 PDT)
- AMBER: a question about xleap WANG,YING (Tue Aug 21 2007 - 12:16:48 PDT)
- AMBER: How to use AMBER Parameter Database ? Qiang Zhong (Wed Aug 22 2007 - 01:53:04 PDT)
- AMBER: MM-PBSA calculations of entropy within the sphere Sergey Samsonov (Wed Aug 22 2007 - 06:49:25 PDT)
- AMBER: xLeap "Could not find type" error WANG,YING (Wed Aug 22 2007 - 07:04:37 PDT)
- AMBER: Running Gaussian to get .out files Lili Peng (Wed Aug 22 2007 - 13:27:25 PDT)
- AMBER: Performance of polarizable model simulations Jones de Andrade (Wed Aug 22 2007 - 21:17:52 PDT)
- AMBER: Parse charges for small molecules Neha Gandhi (Wed Aug 22 2007 - 21:50:38 PDT)
- AMBER: Ca(2+) parameter Qiang Zhong (Thu Aug 23 2007 - 04:01:24 PDT)
- [Fwd: Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj).] Steven Winfield (Thu Aug 23 2007 - 06:31:49 PDT)
- AMBER: Unable to open MDCRD file using vmd priya priya (Thu Aug 23 2007 - 08:04:19 PDT)
- AMBER: How to perform MD simulation in NVT ensemble? WANG,YING (Thu Aug 23 2007 - 09:13:51 PDT)
- AMBER: Prepin error (?) in xleap Lili Peng (Thu Aug 23 2007 - 14:04:03 PDT)
- AMBER: protonation of His residue! Qiang Zhong (Thu Aug 23 2007 - 19:39:51 PDT)
- AMBER: QM/MM in reaction pathways? Qiang Zhong (Fri Aug 24 2007 - 01:00:50 PDT)
- AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 03:19:30 PDT)
- AMBER: SMD simulation Qiang Zhong (Fri Aug 24 2007 - 03:33:41 PDT)
- AMBER: NETCDF Geoff Wood (Fri Aug 24 2007 - 03:43:11 PDT)
- AMBER: articles Beale, John (Fri Aug 24 2007 - 06:02:05 PDT)
- AMBER: PM6? Thomas Patko (CSULB) (Fri Aug 24 2007 - 06:46:16 PDT)
- AMBER: Running Gaussian to get .out files Steve Spronk (Fri Aug 24 2007 - 07:08:13 PDT)
- AMBER: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sat Aug 25 2007 - 10:54:12 PDT)
- AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 00:26:42 PDT)
- AMBER: personal computer configuration for parallel computing emine cebe (Sun Aug 26 2007 - 04:36:28 PDT)
- AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 07:34:57 PDT)
- Fwd: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 23:24:33 PDT)
- AMBER: metalloprotein dynamics Sally Pias (Mon Aug 27 2007 - 10:55:51 PDT)
- AMBER: generating a .rst file from an .mdcrd file Thomas Pochapsky (Mon Aug 27 2007 - 11:41:56 PDT)
- AMBER: Add hydrogen and charge calculation snoze pa (Mon Aug 27 2007 - 12:06:44 PDT)
- AMBER: QM/MM in reaction pathways? Qiang Zhong (Tue Aug 28 2007 - 00:51:30 PDT)
- AMBER: protocols for high pressure simulation brmeher.iitg.ernet.in (Tue Aug 28 2007 - 08:23:00 PDT)
- AMBER: heating up system Francesco Pietra (Tue Aug 28 2007 - 09:16:57 PDT)
- AMBER: energy minimization parameter Qiang Zhong (Wed Aug 29 2007 - 00:54:12 PDT)
- AMBER: refinement of NMR struture using AMBER Prem Prakash Pathak (Wed Aug 29 2007 - 03:57:11 PDT)
- AMBER: Criteria for classical md being OK to move to QM-MM Francesco Pietra (Wed Aug 29 2007 - 09:51:15 PDT)
- AMBER: Schedule for QM-MM with Amber9/Amber10 Francesco Pietra (Wed Aug 29 2007 - 23:30:10 PDT)
- AMBER: RDF unit cell volume BJÖRN KARLSSON (Thu Aug 30 2007 - 01:14:20 PDT)
- AMBER: AMBER at WESTGRID Eduardo Mendez-Villuendas (Thu Aug 30 2007 - 04:49:07 PDT)
- AMBER: bad atom type:F Emilia Wu (Thu Aug 30 2007 - 05:36:14 PDT)
- AMBER: Beale, John (Thu Aug 30 2007 - 06:05:11 PDT)
- AMBER: Fwd: Schedule for QM-MM with Amber9/Amber10 Francesco Pietra (Thu Aug 30 2007 - 06:17:41 PDT)
- AMBER: Squished dimer during transition from NVT to NPT Katrina Lexa (Thu Aug 30 2007 - 14:02:20 PDT)
- AMBER: Connecting two ethanes in LEaP Kliman, Michal (Thu Aug 30 2007 - 13:53:46 PDT)
- AMBER: Scaling for octahedral versus rectilinear boxes David Cerutti (Thu Aug 30 2007 - 22:32:49 PDT)
- AMBER: Confusion about Langevin dymamics Hayden Eastwood (Fri Aug 31 2007 - 06:46:28 PDT)
- AMBER: antechamber question Beale, John (Fri Aug 31 2007 - 07:07:56 PDT)
- AMBER: Converting AMBER-format force fields for tinker Aaron Virshup (Fri Aug 31 2007 - 12:04:12 PDT)
- AMBER: Measuring Bond Angle over simulation Seth Lilavivat (Fri Aug 31 2007 - 12:25:20 PDT)
- AMBER: modified leaprc for glycoproteins Irene Newhouse (Fri Aug 31 2007 - 13:53:05 PDT)
- AMBER: Using ntr=1 in xleap Lili Peng (Fri Aug 31 2007 - 14:27:44 PDT)
- Last message date: Sun Sep 02 2007 - 06:07:39 PDT
- Archived on: Sun Dec 22 2024 - 05:53:38 PST
