Amber Archive May 2008 by thread
- Re: AMBER: calibration of constant pH simulations Pradipta Bandyopadhyay (Wed Apr 30 2008 - 21:02:55 PDT)
- Re: AMBER: regarding segfault during energy minimization Anamika Awasthi (Wed Apr 30 2008 - 22:57:35 PDT)
- Re: AMBER: Cysteine sulphonic acid parameters FyD (Thu May 01 2008 - 05:03:19 PDT)
- AMBER: Discontinuous Constant pH Restarts Neil Bruce (Thu May 01 2008 - 06:41:21 PDT)
- AMBER: Water residue tracking Steve Seibold (Thu May 01 2008 - 09:19:42 PDT)
- AMBER: Installation problem of AMBER on cluster sudipta sinha (Thu May 01 2008 - 11:16:44 PDT)
- AMBER: Amber10 installation error juyong Lee (Thu May 01 2008 - 19:28:07 PDT)
- AMBER: test.parallel.QMMM problem Carra, Claudio (JSC-SK)[USRA] (Fri May 02 2008 - 06:37:28 PDT)
- AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 sychen (Fri May 02 2008 - 07:22:50 PDT)
- AMBER: Help with NMODE Seth Lilavivat (Fri May 02 2008 - 08:24:25 PDT)
- AMBER: cfortran.h error with xlf90 compiler juyong Lee (Fri May 02 2008 - 09:35:32 PDT)
- AMBER: Compiling amber10 with xlf90 fortran compiler juyong Lee (Fri May 02 2008 - 11:27:10 PDT)
- AMBER: Mn2+ parameters in AMBER jitrayut jitonnom (Fri May 02 2008 - 11:46:25 PDT)
- AMBER: Inquiry on B-factor of NMR James Thomas (Fri May 02 2008 - 12:31:09 PDT)
- AMBER: printing dipoles in Amber10 (and earlier) Piotr Cieplak (Fri May 02 2008 - 13:29:49 PDT)
- AMBER: Water tracking Steve Seibold (Fri May 02 2008 - 08:09:35 PDT)
- AMBER: Example .prepi file for nonstandard amino acids finke.oakland.edu (Fri May 02 2008 - 15:00:45 PDT)
- AMBER: about glycam06 WANG,YING (Sat May 03 2008 - 16:22:18 PDT)
- AMBER: Amber10 Installation error - incorrect file suffix juyong Lee (Sun May 04 2008 - 05:46:10 PDT)
- AMBER: Deriving Force Field Parameters Shultz, Jack (Sun May 04 2008 - 14:32:03 PDT)
- AMBER: Jarzinsky relationship E.M. (Sun May 04 2008 - 19:39:51 PDT)
- AMBER: Torsion angle restrains and Jarzinsky E.M. (Mon May 05 2008 - 00:06:56 PDT)
- AMBER: Re: amber 9 compilation problem on IBM SP5 Andrew Emerson (Mon May 05 2008 - 00:57:53 PDT)
- AMBER: Installation error on IBM cluster juyong Lee (Mon May 05 2008 - 01:40:59 PDT)
- AMBER: unable to compile AmberTools 1.0 Rabin (Mon May 05 2008 - 10:07:00 PDT)
- Re: AMBER: error in compilation elsize.cc Scott Brozell (Mon May 05 2008 - 11:55:49 PDT)
- AMBER: About reading in heme and CO molecule together with myoglobin Yang, Lee-Wei (Mon May 05 2008 - 11:08:53 PDT)
- AMBER: AMBER Parallel test error jitrayut jitonnom (Mon May 05 2008 - 11:37:39 PDT)
- AMBER: DCCM correlation analysis Ibrahim Moustafa (Mon May 05 2008 - 13:21:37 PDT)
- AMBER: Units, units units E.M. (Mon May 05 2008 - 15:18:37 PDT)
- AMBER: Minimization in Octahedric Box guardiani.fi.infn.it (Tue May 06 2008 - 04:31:50 PDT)
- AMBER: rmsd per residue Furia Gargano (Tue May 06 2008 - 07:28:59 PDT)
- AMBER: steered MD initial state M. L. Dodson (Tue May 06 2008 - 09:04:09 PDT)
- AMBER: mm_pbsa.pl not reading parameters for nmode Seth Lilavivat (Tue May 06 2008 - 10:50:18 PDT)
- Re: AMBER: Improper dihedral parameters Bill Ross (Tue May 06 2008 - 12:23:55 PDT)
- AMBER: DFTB parameters for O-P Carra, Claudio (JSC-SK)[USRA] (Tue May 06 2008 - 13:01:55 PDT)
- AMBER: Ewald error estimate 欧阳德方 (Wed May 07 2008 - 01:25:22 PDT)
- AMBER: molsurf jacopo.sgrignani.unifi.it (Wed May 07 2008 - 04:11:34 PDT)
- AMBER: uninstall of AMBER sudipta sinha (Wed May 07 2008 - 08:50:37 PDT)
- AMBER: nmode: number of atoms limitation Qi Yan (Wed May 07 2008 - 11:25:58 PDT)
- AMBER: GBSA SA calculation Titus, Jamie \(bairdje\) (Wed May 07 2008 - 11:32:43 PDT)
- AMBER: Hydroxyprolines!!! Titus, Jamie \(bairdje\) (Wed May 07 2008 - 11:54:03 PDT)
- AMBER: Harmonic Force Constant Shultz, Jack (Wed May 07 2008 - 12:32:18 PDT)
- AMBER: How to transfer unformatted coordinates into formatted ones Qi Yan (Wed May 07 2008 - 12:44:10 PDT)
- AMBER: nmode: number of atoms limitation Qi Yan (Wed May 07 2008 - 11:10:48 PDT)
- AMBER: xleap (draw using edit) Taufik Al-Sarraj (Wed May 07 2008 - 19:31:14 PDT)
- AMBER: Compilation of PMEMD sudipta sinha (Thu May 08 2008 - 04:07:28 PDT)
- AMBER: mm_pbsa problem: bad atom type: IP mori.cerm.unifi.it (Thu May 08 2008 - 04:59:12 PDT)
- AMBER: nmode "Atom out of bounds" for min of multiple ligands Seth Lilavivat (Thu May 08 2008 - 07:30:24 PDT)
- AMBER: can amber read .xyz files? WANG,YING (Thu May 08 2008 - 08:29:57 PDT)
- AMBER: velocity autocorrelation function for SPC felxible water model Rahaman, Asif (Thu May 08 2008 - 10:07:41 PDT)
- AMBER: AmberTools on OS X fails tests Hans Martin Senn (Thu May 08 2008 - 11:59:12 PDT)
- AMBER: QM/MM Syed Tarique Moin (Fri May 09 2008 - 01:28:06 PDT)
- AMBER: distance Urszula Uciechowska (Fri May 09 2008 - 07:36:18 PDT)
- AMBER: help to install AMBER9 Jeffrey (Fri May 09 2008 - 07:47:16 PDT)
- AMBER: neutral C-terminus and N-terminus parameters for amber Lisa Perez (Fri May 09 2008 - 10:32:13 PDT)
- AMBER: Prepgen does not give correct result? Rajendra P. OJHA (Fri May 09 2008 - 09:13:58 PDT)
- AMBER: cannot read big .pdb files WANG,YING (Fri May 09 2008 - 19:00:29 PDT)
- AMBER: parmbsc0 parameters for RNA.DNA systems Cenk \(Jenk\) Andac (Sat May 10 2008 - 06:47:50 PDT)
- AMBER: Calculate number of ions Dong Xu (Sat May 10 2008 - 11:32:01 PDT)
- AMBER: Solvent mixture box Francesco Pietra (Sun May 11 2008 - 10:04:52 PDT)
- AMBER: Ewald PARAMETER RANGE WRONG WANG,YING (Sun May 11 2008 - 11:01:09 PDT)
- AMBER: rms Urszula Uciechowska (Mon May 12 2008 - 04:19:41 PDT)
- AMBER: About Hydrophobic Interactions. cgji (Mon May 12 2008 - 09:14:00 PDT)
- AMBER: Problems installing Amber Tools for Amber 10 Sam Danziger (Mon May 12 2008 - 11:20:23 PDT)
- AMBER: Ligand energy minimization Dong Xu (Mon May 12 2008 - 15:07:31 PDT)
- AMBER: nab Rabin (Mon May 12 2008 - 17:40:54 PDT)
- AMBER: from Gromax to AMBER Cristina Sisu (Tue May 13 2008 - 03:00:24 PDT)
- AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222- Catein Catherine (Tue May 13 2008 - 03:17:29 PDT)
- AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params Marcin Krol (Tue May 13 2008 - 06:44:48 PDT)
- AMBER: periodic boundary condition WANG,YING (Tue May 13 2008 - 06:55:00 PDT)
- AMBER: Free Energy Calculations - parameters for MM Seth Lilavivat (Tue May 13 2008 - 09:29:23 PDT)
- AMBER: divcon E.M. (Tue May 13 2008 - 09:58:49 PDT)
- AMBER: Amber10 testing problem Cenk \(Jenk\) Andac (Tue May 13 2008 - 12:46:02 PDT)
- AMBER: simulating the pull out of Carbon Nanotube from polymer with AMBER yuan li (Tue May 13 2008 - 19:53:10 PDT)
- AMBER: MM_PBSA problem in binding_energy mori.cerm.unifi.it (Wed May 14 2008 - 07:17:40 PDT)
- AMBER: about addles:“forrtl: severe (71): integer divide by zero”. 成全 (Wed May 14 2008 - 07:57:25 PDT)
- AMBER: subscribe amber wangluohuaxue (Wed May 14 2008 - 07:40:04 PDT)
- AMBER: simulate dipole moment Qiuting Hong (Wed May 14 2008 - 13:52:33 PDT)
- AMBER: AMBER entropy calculation Thomas Leonard (Wed May 14 2008 - 16:00:45 PDT)
- AMBER: Amber10:Compiling with gcc 2.4.1 yongleli (Thu May 15 2008 - 08:36:29 PDT)
- AMBER: Points on a Sphere Justine Condo (Thu May 15 2008 - 09:27:06 PDT)
- AMBER: MKL libraries/Amber10 Francesco Pietra (Thu May 15 2008 - 11:01:34 PDT)
- AMBER: RESP and Jaguar Seth Lilavivat (Thu May 15 2008 - 13:52:35 PDT)
- AMBER: solvatebox error WANG,YING (Thu May 15 2008 - 14:47:06 PDT)
- AMBER: reading PDB trajectory Mark Abraham (Thu May 15 2008 - 20:49:55 PDT)
- AMBER: PGI amber9 problems Lorenzo Gontrani (Fri May 16 2008 - 02:52:21 PDT)
- AMBER: RESP charges of an unusual substrate Jiayun Pang (Fri May 16 2008 - 03:45:54 PDT)
- AMBER: STEERED MD fatima.chami.durham.ac.uk (Fri May 16 2008 - 09:25:55 PDT)
- AMBER: build proline Qiuting Hong (Fri May 16 2008 - 14:32:47 PDT)
- AMBER: Amber 10 ambpdb bug? Sam Danziger (Sat May 17 2008 - 19:17:44 PDT)
- AMBER: ambertools: static linking of user binaries is not supported on Mac OS X Alan (Mon May 19 2008 - 02:39:32 PDT)
- AMBER: parameters in ff03 and ff99 Peter Kiss (Mon May 19 2008 - 04:21:21 PDT)
- AMBER: Hybrid REMD amber10 Geoff Wood (Mon May 19 2008 - 05:41:54 PDT)
- AMBER: anal Marina Grabar (Mon May 19 2008 - 06:30:13 PDT)
- AMBER: nfft1-3 too large WANG,YING (Mon May 19 2008 - 07:46:51 PDT)
- AMBER: gasteiger is not working with ambertools 1.0 Alan (Mon May 19 2008 - 07:51:05 PDT)
- AMBER: atom type in glycam06 tinni sona (Mon May 19 2008 - 10:06:57 PDT)
- AMBER: bye frustrated modeller (Mon May 19 2008 - 11:29:40 PDT)
- AMBER: analysis REMD rebeca (Mon May 19 2008 - 11:41:15 PDT)
- AMBER: 3rd Annual CMM Workshop on QM/MM Simulations Ross Walker (Mon May 19 2008 - 16:33:55 PDT)
- AMBER: MM-PBSA for carbohydrates Neha Gandhi (Mon May 19 2008 - 19:07:24 PDT)
- AMBER: massively parallel computation Mingfeng Yang (Tue May 20 2008 - 00:03:51 PDT)
- AMBER: xLeap compilation issues Sasha Buzko (Tue May 20 2008 - 16:41:49 PDT)
- AMBER: How to set a ZN atom radius for PB calculations Sam Danziger (Tue May 20 2008 - 17:23:30 PDT)
- AMBER: Regarding binding free energy calculation using MM_PBSA method nag raj (Wed May 21 2008 - 00:01:14 PDT)
- AMBER: $AMBERHOME/dat/slko Francesco Pietra (Wed May 21 2008 - 05:47:59 PDT)
- AMBER: ptraj analyze matrix Seth Lilavivat (Wed May 21 2008 - 07:53:28 PDT)
- AMBER: amber tools installation vijayaraj.clri.info (Wed May 21 2008 - 08:22:37 PDT)
- AMBER: pressure regulation methods Vlad Cojocaru (Wed May 21 2008 - 09:25:08 PDT)
- AMBER: ff99 and ff03 forcefield parameters Peter Kiss (Wed May 21 2008 - 14:01:47 PDT)
- AMBER: Parallel Self-guided Langevin simulation Dirar Homouz (Wed May 21 2008 - 15:23:27 PDT)
- AMBER: about hydrogen bond in amber force field WANG,YING (Wed May 21 2008 - 19:24:47 PDT)
- AMBER: COM RESTRAINT fatima.chami.durham.ac.uk (Thu May 22 2008 - 05:17:09 PDT)
- AMBER: potassium ion Lars Skjærven (Thu May 22 2008 - 06:09:59 PDT)
- AMBER: amber10 installation vijayaraj.clri.info (Thu May 22 2008 - 07:22:47 PDT)
- AMBER: AMBER file preparation for protein-carbohydrate complex Neha Gandhi (Thu May 22 2008 - 07:31:50 PDT)
- AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system Pavan G (Thu May 22 2008 - 08:37:56 PDT)
- Re: AMBER: potassium ion Bill Ross (Thu May 22 2008 - 11:27:21 PDT)
- AMBER: Calculate the RESP charge Fe3+ of heme (p450) chen bents (Thu May 22 2008 - 19:16:12 PDT)
- AMBER: self-diffusion coefficient and Berendsen Jennifer.Thomas.cbt.uhp-nancy.fr (Fri May 23 2008 - 01:03:49 PDT)
- AMBER: help MD running error Qiuting Hong (Fri May 23 2008 - 01:40:12 PDT)
- AMBER: PBC in 2D fatima.chami.durham.ac.uk (Fri May 23 2008 - 06:13:39 PDT)
- AMBER: how generate the final output file using mmpbsa luzhenw1.msu.edu (Fri May 23 2008 - 13:49:33 PDT)
- AMBER: how to extract energy WANG,YING (Fri May 23 2008 - 18:08:13 PDT)
- AMBER: periodic bondary condition WANG,YING (Fri May 23 2008 - 18:16:34 PDT)
- AMBER: ptraj mask not working with psf file Dong Xu (Fri May 23 2008 - 19:53:27 PDT)
- AMBER: Amber9 vs Amber10+MKL benchmark Francesco Pietra (Sat May 24 2008 - 06:48:12 PDT)
- AMBER: Fw: Amber9 vs Amber10+MKL benchmark Francesco Pietra (Sat May 24 2008 - 06:51:53 PDT)
- AMBER: calculating the energy from the restart file priya priya (Sat May 24 2008 - 07:03:46 PDT)
- AMBER: Fw: Amber9 vs Amber10+MKL benchmark Francesco Pietra (Sat May 24 2008 - 07:50:45 PDT)
- AMBER: caculating nonpolar solvation energies ke dong (Sat May 24 2008 - 07:53:17 PDT)
- AMBER: trajectories into trajectory Hakkim Boy (Sun May 25 2008 - 04:30:22 PDT)
- AMBER: mass weighted rms fit Dong Xu (Sun May 25 2008 - 09:11:43 PDT)
- AMBER: using amber ports in gromacs Cristina Sisu (Sun May 25 2008 - 11:22:58 PDT)
- AMBER: is in vacuo simulation neccessary? Anamika Awasthi (Sun May 25 2008 - 22:18:58 PDT)
- AMBER: Umbrella Sampling for proteins German Erlenkamp (Mon May 26 2008 - 02:23:56 PDT)
- AMBER: peptide at the box center during NVT-MD Darek Czapiewski (Mon May 26 2008 - 03:01:45 PDT)
- AMBER: B-factor calculation from data with different write frequencies Sally Pias (Mon May 26 2008 - 21:19:42 PDT)
- AMBER: Which is best temperature controlling method sudipta sinha (Tue May 27 2008 - 03:25:02 PDT)
- Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross (Tue May 27 2008 - 09:44:23 PDT)
- AMBER: error when read inpcrd WANG,YING (Tue May 27 2008 - 13:32:02 PDT)
- AMBER: bugfix (imin=5) in amber9 Xioling Chuang (Tue May 27 2008 - 21:23:09 PDT)
- AMBER: compilation problem with AMBER10 bhargav patel (Tue May 27 2008 - 22:56:15 PDT)
- AMBER: Hydration free energies of charged ions using PME Markus Kaukonen (Tue May 27 2008 - 23:51:26 PDT)
- AMBER: install amber tools Alejandro Valbuena (Wed May 28 2008 - 03:14:35 PDT)
- AMBER: Segmentation faults trying to run sander mpi Idan Gabdank (Wed May 28 2008 - 03:59:09 PDT)
- AMBER: restarting molecular dynamics Germain Vallverdu (Wed May 28 2008 - 06:18:16 PDT)
- AMBER: mbondi radii for gaff atom types Sara J (Wed May 28 2008 - 08:03:52 PDT)
- AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error Kateryna Miroshnychenko (Wed May 28 2008 - 08:08:19 PDT)
- AMBER: protonate in Amber10 Benjamin Juhl (Wed May 28 2008 - 07:55:06 PDT)
- AMBER: rmsd vs frame Francesco Pietra (Wed May 28 2008 - 15:56:24 PDT)
- AMBER: Fw: rmsd vs frame Francesco Pietra (Wed May 28 2008 - 16:19:11 PDT)
- AMBER: VMD Movie Campbell, Patrick (Wed May 28 2008 - 16:33:39 PDT)
- AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Wed May 28 2008 - 22:56:48 PDT)
- AMBER: ligand unit charge is not zero amor san juan (Thu May 29 2008 - 01:44:58 PDT)
- AMBER: solvatebox fatima.chami.durham.ac.uk (Thu May 29 2008 - 04:46:42 PDT)
- AMBER: Installing PMEMD with Amber10 Justin A. Lemkul (Thu May 29 2008 - 06:23:05 PDT)
- AMBER: VMD Movie 2 Campbell, Patrick (Thu May 29 2008 - 10:39:20 PDT)
- AMBER: ptraj rmsd calculation Pavan G (Thu May 29 2008 - 11:08:36 PDT)
- AMBER: VMD Movie 3 Campbell, Patrick (Thu May 29 2008 - 11:12:20 PDT)
- AMBER: VMD Movie 4 Campbell, Patrick (Thu May 29 2008 - 12:37:43 PDT)
- AMBER: ptraj has trouble with x-plor psf file from VMD Dong Xu (Thu May 29 2008 - 13:23:56 PDT)
- AMBER: Ptraj | Multiple trajout commands? Ian (Fri May 30 2008 - 01:39:23 PDT)
- AMBER: Jarzynski fatima.chami.durham.ac.uk (Fri May 30 2008 - 04:44:41 PDT)
- AMBER: nab Joachim Reichelt (Fri May 30 2008 - 02:48:56 PDT)
- AMBER: Iron-Sulfur Cluster Joachim Reichelt (Fri May 30 2008 - 02:46:30 PDT)
- AMBER: Sander instead of PMEMD Cristina Sisu (Fri May 30 2008 - 06:47:13 PDT)
- AMBER: VMD Movie 3 Campbell, Patrick (Fri May 30 2008 - 07:56:41 PDT)
- AMBER: tleap error message Wang,Ying (Fri May 30 2008 - 09:08:14 PDT)
- AMBER: igb and ibelly Holly Freedman (Fri May 30 2008 - 12:23:21 PDT)
- AMBER: SANDER and PMEMD with openmpi Ross Walker (Fri May 30 2008 - 15:18:04 PDT)
- AMBER: MMPBSA error Cristina Sisu (Sat May 31 2008 - 07:00:08 PDT)
- AMBER: ptraj analyze modes from nmode Miguel Ortiz-Lombardía (Sat May 31 2008 - 08:40:50 PDT)
- Re: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Francesco Pietra (Sat May 31 2008 - 11:31:04 PDT)
- AMBER: amber9 , ptraj vector commad issue Vijay Singh (Sat May 31 2008 - 16:34:23 PDT)
- Last message date: Sun Jun 01 2008 - 06:08:25 PDT
- Archived on: Fri Nov 22 2024 - 05:53:39 PST
