AMBER Archive (2007) - Aug 2007 By ThreadMost recent messages
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Starting: Wed Aug 01 2007 - 04:36:31 CDT
Ending: Fri Aug 31 2007 - 20:14:32 CDT
- AMBER: how to calculate the ps/day of md simulation using using my cluster system in amber7 Syed Tarique Moin (Wed Aug 01 2007 - 04:36:31 CDT)
- AMBER: problem compiling Amber9 on 64-machine fatima.chami_at_durham.ac.uk (Wed Aug 01 2007 - 06:03:48 CDT)
- Fwd: RE: AMBER: Average potential energies and conformer ratios Francesco Pietra (Wed Aug 01 2007 - 08:58:02 CDT)
- AMBER: Problem with Antechamber and point charges anna duraj (Wed Aug 01 2007 - 14:40:44 CDT)
- AMBER: neutral terminals Jena M (Wed Aug 01 2007 - 19:15:46 CDT)
- Re: AMBER: bugfix for impropers in parmchk Jiten (Wed Aug 01 2007 - 23:02:24 CDT)
- AMBER: Problem with antechamber Anju Sharma (Thu Aug 02 2007 - 01:34:39 CDT)
- AMBER: (no subject) Syed Tarique Moin (Thu Aug 02 2007 - 01:50:59 CDT)
- AMBER: planarity restraints for NA Seth Lilavivat (Thu Aug 02 2007 - 08:12:18 CDT)
- AMBER: restrained md and mm pbsa Christopher Gaughan (Thu Aug 02 2007 - 09:15:17 CDT)
- AMBER: vector corrplane Servaas Michielssens (Thu Aug 02 2007 - 10:25:45 CDT)
- AMBER: Force Field Parameters Beale, John (Thu Aug 02 2007 - 11:46:16 CDT)
- AMBER: Calculating cumulative average Francesco Pietra (Thu Aug 02 2007 - 12:00:10 CDT)
- AMBER: edit.out amber version 9 Greg Gannon (Thu Aug 02 2007 - 13:21:31 CDT)
- AMBER: Problem generating .prepin file in Antechamber Lili Peng (Thu Aug 02 2007 - 14:07:11 CDT)
- AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Thu Aug 02 2007 - 19:33:40 CDT)
- Re: AMBER: Antechamber formal charges with Gasteiger method Scott Brozell (Thu Aug 02 2007 - 20:44:28 CDT)
- AMBER: Information about Amber 9 Lycourgos Chiniadis (Fri Aug 03 2007 - 00:11:17 CDT)
- AMBER: force field for hydrogels Prem Prakash Pathak (Fri Aug 03 2007 - 01:03:48 CDT)
- AMBER: unable to save prmtop/inpcrd for chcl3box Francesco Pietra (Fri Aug 03 2007 - 05:09:03 CDT)
- AMBER: Successful compile on Mac OSX + Intel compilers Viv Kendon (Fri Aug 03 2007 - 07:28:56 CDT)
- AMBER: Fwd: unable to save prmtop/inpcrd for chcl3box Francesco Pietra (Fri Aug 03 2007 - 07:24:24 CDT)
- AMBER: Binary file curiosities David LeBard (Fri Aug 03 2007 - 17:59:45 CDT)
- AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sat Aug 04 2007 - 03:32:40 CDT)
- AMBER: nucleic acid electrostatic energy Tiago Sobreira (Sat Aug 04 2007 - 08:45:46 CDT)
- AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sat Aug 04 2007 - 09:33:35 CDT)
- AMBER: GAFF atom typing for flavin Hans Martin Senn (Sat Aug 04 2007 - 11:15:30 CDT)
- AMBER: force field for irregulate DNA ends Hu, Shaowen (JSC-SK)[USRA] (Sat Aug 04 2007 - 13:20:42 CDT)
- AMBER: setting dimensions of truncated octahedron Lillian chong (Sat Aug 04 2007 - 15:34:59 CDT)
- AMBER: RE: tutorial file polyAT_vac.prmtop Ross Walker (Sun Aug 05 2007 - 22:09:46 CDT)
- AMBER: Problem while carrying out minimisation of drug molecule using sander Anju Sharma (Sun Aug 05 2007 - 22:51:11 CDT)
- AMBER: Specific heat graph is a straight line priya priya (Mon Aug 06 2007 - 08:33:52 CDT)
- AMBER: Integrating the alpha-helix bias correction into ff94 Andrew Borgert (Mon Aug 06 2007 - 14:18:58 CDT)
- AMBER: hybridization in Amber, pertaining to resonant structures, ions Karen Callahan (Mon Aug 06 2007 - 23:13:27 CDT)
- AMBER: heical content in simulations priya priya (Tue Aug 07 2007 - 02:58:12 CDT)
- AMBER: Problem with minimization Syed Tarique Moin (Tue Aug 07 2007 - 08:11:32 CDT)
- AMBER: compile amber8 with mpich2 Kailee (Tue Aug 07 2007 - 08:18:14 CDT)
- AMBER: Positive EPtot in QM-MM Francesco Pietra (Tue Aug 07 2007 - 09:34:35 CDT)
- AMBER: about shake linfu (Tue Aug 07 2007 - 20:36:59 CDT)
- AMBER: msubhamoy_at_ibab.ac.in (Wed Aug 08 2007 - 08:01:00 CDT)
- AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA msubhamoy_at_ibab.ac.in (Wed Aug 08 2007 - 08:08:04 CDT)
- AMBER: RE: TUTORIAL B1 file polyAT_vac.prmtop Ross Walker (Wed Aug 08 2007 - 09:52:39 CDT)
- AMBER: RE: Problem loading pdf into tleap Ross Walker (Wed Aug 08 2007 - 12:29:19 CDT)
- AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 16:33:22 CDT)
- Re: AMBER: Cygwin error Bill Ross (Wed Aug 08 2007 - 16:43:49 CDT)
- AMBER: how to combine two molecules Wenyong Tong (Thu Aug 09 2007 - 00:34:33 CDT)
- AMBER: NVE energy and temperature drift Nikola Trbovic (Thu Aug 09 2007 - 15:24:11 CDT)
- AMBER: Implicit solvent simulation is too slow. SeungPyo Hong (Fri Aug 10 2007 - 07:42:11 CDT)
- AMBER: How to couple only one residue to the temperature bath? Michael Lerner (Fri Aug 10 2007 - 09:45:10 CDT)
- AMBER: short 2'OH-OP contacts in RNA Jose Gallego (Fri Aug 10 2007 - 11:22:35 CDT)
- AMBER: vlimit exceeded for the step Sudha Mani Karra (Fri Aug 10 2007 - 14:31:08 CDT)
- AMBER: Steve Seibold (Fri Aug 10 2007 - 15:17:47 CDT)
- AMBER: Citation for Langevin thermostat? Marc Baaden (Sat Aug 11 2007 - 02:13:28 CDT)
- AMBER: Using charmm force field in amber Seongeun Yang (Sat Aug 11 2007 - 03:44:44 CDT)
- AMBER: Failure to SCF convergence Francesco Pietra (Sat Aug 11 2007 - 11:56:53 CDT)
- AMBER: imin=5 and inptraj Nikola Trbovic (Sat Aug 11 2007 - 15:11:08 CDT)
- AMBER: Neutralize charges for simulated annealing? Francesco Pietra (Sat Aug 11 2007 - 17:35:30 CDT)
- AMBER: setbox command error priya priya (Mon Aug 13 2007 - 11:18:16 CDT)
- AMBER: unsubscribe Pan, Yongmei (Mon Aug 13 2007 - 12:35:12 CDT)
- AMBER: Using TLEAP to set up MD in the crystal lattice space? David Cerutti (Mon Aug 13 2007 - 16:09:51 CDT)
- AMBER: Normal Mode Analysis Kresimir Sikic (Mon Aug 13 2007 - 10:12:59 CDT)
- AMBER: Machine environment to install AMBER 8 M. Maeda (Tue Aug 14 2007 - 01:03:07 CDT)
- AMBER: regarding implicit simulation gurpreet singh (Tue Aug 14 2007 - 01:21:35 CDT)
- AMBER: MMPBSA NOT Getting results msubhamoy_at_ibab.ac.in (Tue Aug 14 2007 - 03:26:57 CDT)
- AMBER: How to carry out drug-dna complex simulations Anju Sharma (Tue Aug 14 2007 - 03:50:04 CDT)
- AMBER: Tutorial about SMD? Qiang Zhong (Tue Aug 14 2007 - 05:19:09 CDT)
- AMBER: Parallelizin antechamber? Francesco Pietra (Tue Aug 14 2007 - 08:29:11 CDT)
- AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 15:31:34 CDT)
- AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 03:43:45 CDT)
- AMBER: Building parallel Amber 9.0 Beale, John (Wed Aug 15 2007 - 07:21:56 CDT)
- AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra (Wed Aug 15 2007 - 09:38:06 CDT)
- AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade (Wed Aug 15 2007 - 11:50:57 CDT)
- AMBER: docking ability anna duraj (Wed Aug 15 2007 - 12:34:37 CDT)
- AMBER: Bug in ptraj mask processing? Steve Spronk (Wed Aug 15 2007 - 14:18:15 CDT)
- AMBER: Missplaced TERs Steve Seibold (Thu Aug 16 2007 - 13:35:26 CDT)
- AMBER: What is the best computer for running AMBER simulations? Lili Peng (Thu Aug 16 2007 - 16:37:03 CDT)
- AMBER: NAN and vlimit exceeded errors in restrained MD.. using IBELLY Sandeep Kaushik (Fri Aug 17 2007 - 00:44:17 CDT)
- AMBER: Thermodynamic Integration for a CHARGED molecule ming hui (Fri Aug 17 2007 - 04:12:38 CDT)
- AMBER: MPI Beale, John (Fri Aug 17 2007 - 07:00:33 CDT)
- AMBER: Molsurf error Pankaj R. Daga (Fri Aug 17 2007 - 12:46:54 CDT)
- AMBER: ptraj hydrogen bonding defaults Michael Lerner (Fri Aug 17 2007 - 17:26:09 CDT)
- AMBER: DFTB email address Francesco Pietra (Sat Aug 18 2007 - 02:14:53 CDT)
- AMBER: charges in PBSA calculation Neha Gandhi (Sat Aug 18 2007 - 21:20:16 CDT)
- AMBER: CRESP charges in antechamber prepin Francesco Pietra (Mon Aug 20 2007 - 02:23:24 CDT)
- AMBER: mmpbsa calculation msubhamoy_at_ibab.ac.in (Mon Aug 20 2007 - 04:53:42 CDT)
- AMBER: TEST_FAILURES Qiang Zhong (Mon Aug 20 2007 - 07:59:28 CDT)
- AMBER: Entropy in MM_PBSA Sergey Samsonov (Mon Aug 20 2007 - 10:01:37 CDT)
- AMBER: Beale, John (Mon Aug 20 2007 - 10:41:06 CDT)
- AMBER: $tleap is not normal Qiang Zhong (Mon Aug 20 2007 - 20:34:00 CDT)
- AMBER: Regarding free energy calculation and covalent bond nag raj (Mon Aug 20 2007 - 23:07:04 CDT)
- AMBER: Error in MMPBSA Calculation msubhamoy_at_ibab.ac.in (Tue Aug 21 2007 - 00:53:17 CDT)
- AMBER: command tleap is not normal Qiang Zhong (Tue Aug 21 2007 - 03:12:44 CDT)
- AMBER: how to include mpirun in this script Syed Tarique Moin (Tue Aug 21 2007 - 05:50:12 CDT)
- AMBER: How to use AMBER Parameter Database ? Qiang Zhong (Tue Aug 21 2007 - 07:36:46 CDT)
- AMBER: Thermodynamic Integration for conformational changes? Francesco Pietra (Tue Aug 21 2007 - 11:57:47 CDT)
- AMBER: xLeap "Could not find type" error Lili Peng (Tue Aug 21 2007 - 14:28:46 CDT)
- AMBER: Octahedral box orientation David Cerutti (Tue Aug 21 2007 - 08:08:38 CDT)
- AMBER: Force field for RNA with U-turn motif Cenk Andac (Tue Aug 21 2007 - 08:52:48 CDT)
- AMBER: Tutorial of document about QM/MM in reaction pathways? Qiang Zhong (Tue Aug 21 2007 - 09:06:53 CDT)
- AMBER: a question about xleap WANG,YING (Tue Aug 21 2007 - 14:16:48 CDT)
- AMBER: How to use AMBER Parameter Database ? Qiang Zhong (Wed Aug 22 2007 - 03:53:04 CDT)
- AMBER: MM-PBSA calculations of entropy within the sphere Sergey Samsonov (Wed Aug 22 2007 - 08:49:25 CDT)
- AMBER: xLeap "Could not find type" error WANG,YING (Wed Aug 22 2007 - 09:04:37 CDT)
- AMBER: Running Gaussian to get .out files Lili Peng (Wed Aug 22 2007 - 15:27:25 CDT)
- AMBER: Performance of polarizable model simulations Jones de Andrade (Wed Aug 22 2007 - 23:17:52 CDT)
- AMBER: Parse charges for small molecules Neha Gandhi (Wed Aug 22 2007 - 23:50:38 CDT)
- AMBER: Ca(2+) parameter Qiang Zhong (Thu Aug 23 2007 - 06:01:24 CDT)
- [Fwd: Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj).] Steven Winfield (Thu Aug 23 2007 - 08:31:49 CDT)
- AMBER: Unable to open MDCRD file using vmd priya priya (Thu Aug 23 2007 - 10:04:19 CDT)
- AMBER: How to perform MD simulation in NVT ensemble? WANG,YING (Thu Aug 23 2007 - 11:13:51 CDT)
- AMBER: Prepin error (?) in xleap Lili Peng (Thu Aug 23 2007 - 16:04:03 CDT)
- AMBER: protonation of His residue! Qiang Zhong (Thu Aug 23 2007 - 21:39:51 CDT)
- AMBER: QM/MM in reaction pathways? Qiang Zhong (Fri Aug 24 2007 - 03:00:50 CDT)
- AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 05:19:30 CDT)
- AMBER: SMD simulation Qiang Zhong (Fri Aug 24 2007 - 05:33:41 CDT)
- AMBER: NETCDF Geoff Wood (Fri Aug 24 2007 - 05:43:11 CDT)
- AMBER: articles Beale, John (Fri Aug 24 2007 - 08:02:05 CDT)
- AMBER: PM6? Thomas Patko (CSULB) (Fri Aug 24 2007 - 08:46:16 CDT)
- AMBER: Running Gaussian to get .out files Steve Spronk (Fri Aug 24 2007 - 09:08:13 CDT)
- AMBER: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sat Aug 25 2007 - 12:54:12 CDT)
- AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 02:26:42 CDT)
- AMBER: personal computer configuration for parallel computing emine cebe (Sun Aug 26 2007 - 06:36:28 CDT)
- AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 09:34:57 CDT)
- Fwd: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Mon Aug 27 2007 - 01:24:33 CDT)
- AMBER: metalloprotein dynamics Sally Pias (Mon Aug 27 2007 - 12:55:51 CDT)
- AMBER: generating a .rst file from an .mdcrd file Thomas Pochapsky (Mon Aug 27 2007 - 13:41:56 CDT)
- AMBER: Add hydrogen and charge calculation snoze pa (Mon Aug 27 2007 - 14:06:44 CDT)
- AMBER: QM/MM in reaction pathways? Qiang Zhong (Tue Aug 28 2007 - 02:51:30 CDT)
- AMBER: protocols for high pressure simulation brmeher_at_iitg.ernet.in (Tue Aug 28 2007 - 10:23:00 CDT)
- AMBER: heating up system Francesco Pietra (Tue Aug 28 2007 - 11:16:57 CDT)
- AMBER: energy minimization parameter Qiang Zhong (Wed Aug 29 2007 - 02:54:12 CDT)
- AMBER: refinement of NMR struture using AMBER Prem Prakash Pathak (Wed Aug 29 2007 - 05:57:11 CDT)
- AMBER: Criteria for classical md being OK to move to QM-MM Francesco Pietra (Wed Aug 29 2007 - 11:51:15 CDT)
- AMBER: Schedule for QM-MM with Amber9/Amber10 Francesco Pietra (Thu Aug 30 2007 - 01:30:10 CDT)
- AMBER: RDF unit cell volume BJÖRN KARLSSON (Thu Aug 30 2007 - 03:14:20 CDT)
- AMBER: AMBER at WESTGRID Eduardo Mendez-Villuendas (Thu Aug 30 2007 - 06:49:07 CDT)
- AMBER: bad atom type:F Emilia Wu (Thu Aug 30 2007 - 07:36:14 CDT)
- AMBER: Beale, John (Thu Aug 30 2007 - 08:05:11 CDT)
- AMBER: Fwd: Schedule for QM-MM with Amber9/Amber10 Francesco Pietra (Thu Aug 30 2007 - 08:17:41 CDT)
- AMBER: Connecting two ethanes in LEaP Kliman, Michal (Thu Aug 30 2007 - 15:53:46 CDT)
- AMBER: Squished dimer during transition from NVT to NPT Katrina Lexa (Thu Aug 30 2007 - 16:02:20 CDT)
- AMBER: Scaling for octahedral versus rectilinear boxes David Cerutti (Fri Aug 31 2007 - 00:32:49 CDT)
- AMBER: Confusion about Langevin dymamics Hayden Eastwood (Fri Aug 31 2007 - 08:46:28 CDT)
- AMBER: antechamber question Beale, John (Fri Aug 31 2007 - 09:07:56 CDT)
- AMBER: Converting AMBER-format force fields for tinker Aaron Virshup (Fri Aug 31 2007 - 14:04:12 CDT)
- AMBER: Measuring Bond Angle over simulation Seth Lilavivat (Fri Aug 31 2007 - 14:25:20 CDT)
- AMBER: modified leaprc for glycoproteins Irene Newhouse (Fri Aug 31 2007 - 15:53:05 CDT)
- AMBER: Using ntr=1 in xleap Lili Peng (Fri Aug 31 2007 - 16:27:44 CDT)
Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:09 CST
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