AMBER Archive (2009) - Aug 2009 By ThreadMost recent messages
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Starting: Sat Aug 01 2009 - 00:33:58 CDT
Ending: Mon Aug 31 2009 - 23:48:39 CDT
- [AMBER] radial distribution function Dharmik Meghana shankar (Sat Aug 01 2009 - 00:33:58 CDT)
- [AMBER] Timescales and restraints for protein-small ligands movement simulations Andrew Voronkov (Sat Aug 01 2009 - 01:23:19 CDT)
- [AMBER] Showing error bharat lakhani (Sat Aug 01 2009 - 08:12:00 CDT)
- [AMBER] Showing error in energy minimization bharat lakhani (Sun Aug 02 2009 - 01:22:30 CDT)
- [AMBER] showing error when creating topology and coordinate file bharat lakhani (Mon Aug 03 2009 - 02:19:59 CDT)
- [AMBER] optimization step length ondrej.prenosil_at_marge.uochb.cas.cz (Mon Aug 03 2009 - 05:40:15 CDT)
- [AMBER] Problem with Amber8 Sebastian Petruczynik (Mon Aug 03 2009 - 08:28:56 CDT)
- [AMBER] What is the meaning of IED values for PCA analysis? Catein Catherine (Mon Aug 03 2009 - 09:30:15 CDT)
- [AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Jianping Lin (Mon Aug 03 2009 - 09:57:28 CDT)
- [AMBER] Lennard Jones potential Rizwan Tai (Mon Aug 03 2009 - 12:13:16 CDT)
- [AMBER] parmchk problem isaac sugden (Tue Aug 04 2009 - 09:12:29 CDT)
- Re: [AMBER] Protein Activity Bill Ross (Tue Aug 04 2009 - 14:19:32 CDT)
- [AMBER] problem of mm_pbsa Qinghua Liao (Wed Aug 05 2009 - 00:46:51 CDT)
- [AMBER] USE A VERSION COMPILED WITHOUT -DLES s. Bill (Wed Aug 05 2009 - 05:50:01 CDT)
- [AMBER] TWO restraints with different force constants s. Bill (Wed Aug 05 2009 - 06:54:18 CDT)
- AW: [AMBER] TWO restraints with different force constants Aust, Susanne (Wed Aug 05 2009 - 07:31:38 CDT)
- [AMBER] Computational Resources s. Bill (Wed Aug 05 2009 - 10:17:34 CDT)
- [AMBER] ptraj failure to parse psf input Sasha Buzko (Wed Aug 05 2009 - 11:39:57 CDT)
- [AMBER] nmode output Vahdati N. (Wed Aug 05 2009 - 17:26:11 CDT)
- [AMBER] implicit solvent simulation Manish Kumar (Wed Aug 05 2009 - 23:49:30 CDT)
- [AMBER] Model(l)ing'09 in Erlangen, Germany: Registration Open Until August 31st Harald Lanig (Thu Aug 06 2009 - 03:39:07 CDT)
- [AMBER] Extreme optimization problems ondrej.prenosil_at_marge.uochb.cas.cz (Thu Aug 06 2009 - 07:04:09 CDT)
- [AMBER] parameters for HIV protease inhibitors Oliver Kuhn (Thu Aug 06 2009 - 09:51:03 CDT)
- [AMBER] Regd : gaff force field KIRTANA S (Thu Aug 06 2009 - 15:09:14 CDT)
- [AMBER] How to keep the closest solvent mols to each atoms by PTRAJ? u8613020_at_msg.ndhu.edu.tw (Thu Aug 06 2009 - 20:40:17 CDT)
- [AMBER] implicit solvent simulation with new ligand Manish Kumar (Thu Aug 06 2009 - 22:29:37 CDT)
- [AMBER] query bharat lakhani (Fri Aug 07 2009 - 04:11:42 CDT)
- [AMBER] pmemd michael (Fri Aug 07 2009 - 04:50:29 CDT)
- [AMBER] query regarding resp subarna thakur (Fri Aug 07 2009 - 07:14:35 CDT)
- [AMBER] (no subject) Beale, John (Fri Aug 07 2009 - 07:16:58 CDT)
- [AMBER] MM-PBSA results Dmitry Osolodkin (Fri Aug 07 2009 - 09:31:48 CDT)
- [AMBER] Appropriate nmode input file for gas and vacuum phase simulation Scott Pendley (Fri Aug 07 2009 - 12:48:52 CDT)
- [AMBER] antechamber am1-bcc issues David Mobley (Fri Aug 07 2009 - 13:19:53 CDT)
- [AMBER] Error in equilibration: file _ew_box.f Biswaranjan Meher (Fri Aug 07 2009 - 15:39:00 CDT)
- [AMBER] Why..QM/MM s. Bill (Sat Aug 08 2009 - 06:26:46 CDT)
- [AMBER] hydrogen bond? Jio M (Sun Aug 09 2009 - 06:29:23 CDT)
- [AMBER] Regarding Minimization maxcyc Ashish Runthala (Sun Aug 09 2009 - 09:09:58 CDT)
- [AMBER] DivCon - QM/MM s. Bill (Mon Aug 10 2009 - 09:11:39 CDT)
- [AMBER] Any Comment, please s. Bill (Tue Aug 11 2009 - 02:56:20 CDT)
- AW: [AMBER] Any Comment, please Aust, Susanne (Tue Aug 11 2009 - 03:17:18 CDT)
- AW: AW: [AMBER] Any Comment, please Aust, Susanne (Tue Aug 11 2009 - 03:36:34 CDT)
- [AMBER] Amber99SB eric johnson (Tue Aug 11 2009 - 09:33:34 CDT)
- [AMBER] suggestions pls Jio M (Tue Aug 11 2009 - 12:44:19 CDT)
- [AMBER] query regarding fes cluster subarna thakur (Wed Aug 12 2009 - 00:39:55 CDT)
- [AMBER] gaussian 98 input/output for antechamber/resp wong105_at_llnl.gov (Wed Aug 12 2009 - 13:41:45 CDT)
- [AMBER] REMD using hybrid solvent model Morad Mustafa (Wed Aug 12 2009 - 14:05:40 CDT)
- [AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB Manish Kumar (Wed Aug 12 2009 - 14:44:37 CDT)
- [Amber]: REMD using hybrid solvent model Morad Mustafa (Wed Aug 12 2009 - 16:30:01 CDT)
- [AMBER] sourcing leap commands in log file Donald Keidel (Wed Aug 12 2009 - 19:32:31 CDT)
- Re: [AMBER] sourcing leap commands in log file Bill Ross (Wed Aug 12 2009 - 19:47:57 CDT)
- [AMBER] reset velocity Parimal Kar (Wed Aug 12 2009 - 20:01:33 CDT)
- [AMBER] ptraj imaging of namd generated trajectories Vlad Cojocaru (Thu Aug 13 2009 - 04:35:49 CDT)
- [AMBER] ptraj-image Nancy (Thu Aug 13 2009 - 05:35:01 CDT)
- [AMBER] box problem Nancy (Thu Aug 13 2009 - 06:20:20 CDT)
- [AMBER] NAB optimization ondrej.prenosil_at_marge.uochb.cas.cz (Thu Aug 13 2009 - 08:45:26 CDT)
- [AMBER] drying of solvent possible ? Jio M (Thu Aug 13 2009 - 08:49:00 CDT)
- [AMBER] Strange QM/MM Divcon - help me out s. Bill (Thu Aug 13 2009 - 10:37:54 CDT)
- [AMBER] QM/MM types. ros_at_servidor.unam.mx (Thu Aug 13 2009 - 10:49:02 CDT)
- Re: [AMBER] drying of solvent possible ? Bill Ross (Thu Aug 13 2009 - 11:21:35 CDT)
- [AMBER] Charge Problem s. Bill (Fri Aug 14 2009 - 03:25:05 CDT)
- [AMBER] MM_PBSA not successful workalemahu berhanu (Fri Aug 14 2009 - 16:45:41 CDT)
- [AMBER] AMBER job restart problem Kefa Lu (Sat Aug 15 2009 - 03:22:08 CDT)
- [AMBER] AMBER on a Mac Mini cluster PoC Abdul Rehman Gani (Sun Aug 16 2009 - 10:51:44 CDT)
- [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj workalemahu berhanu (Sun Aug 16 2009 - 15:13:21 CDT)
- [AMBER] gaussain output subarna thakur (Mon Aug 17 2009 - 02:11:00 CDT)
- [AMBER] [AmberTool] xleap problem ÁÖżº (Mon Aug 17 2009 - 03:57:37 CDT)
- [AMBER] amber 10 test fails with pathscale 3.2 Raj (Mon Aug 17 2009 - 07:54:45 CDT)
- Re: [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj workalemahu berhanu (Mon Aug 17 2009 - 08:26:35 CDT)
- [AMBER] amber test fails with ICC 11.0.081 Raj (Mon Aug 17 2009 - 09:57:57 CDT)
- [AMBER] Can i link and refine two domains of a single protein Ashish Runthala (Mon Aug 17 2009 - 10:32:33 CDT)
- [AMBER] Re: [q4md-fft] charge calculation FyD (Mon Aug 17 2009 - 18:40:49 CDT)
- [AMBER] AMBER is running silently Kefa Lu (Mon Aug 17 2009 - 17:47:34 CDT)
- Re: [AMBER] AMBER is running silently Bill Ross (Mon Aug 17 2009 - 18:04:02 CDT)
- [AMBER] antechamber execution subarna thakur (Tue Aug 18 2009 - 01:06:52 CDT)
- [AMBER] Can i link and refine the modeled domains with different proteins bound on it Ashish Runthala (Tue Aug 18 2009 - 06:13:23 CDT)
- [AMBER] RDC import from PALES Thomas Pochapsky (Tue Aug 18 2009 - 09:33:42 CDT)
- [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? Jose Borreguero (Tue Aug 18 2009 - 09:37:39 CDT)
- [AMBER] ***PROBLEMS WITH GROUPLRES Maria Mirza (Tue Aug 18 2009 - 19:34:41 CDT)
- [AMBER] Distance restraint and periodic boundary conditions Cyril Falvo (Tue Aug 18 2009 - 19:58:29 CDT)
- [AMBER] RESP charges of Fe4S4 cluster subarna thakur (Wed Aug 19 2009 - 02:53:20 CDT)
- AW: [AMBER] Conference or workshop on AMBER? Aust, Susanne (Wed Aug 19 2009 - 03:16:21 CDT)
- [AMBER] resp calculation for rubredoxin vhakkim boy (Wed Aug 19 2009 - 05:11:22 CDT)
- [AMBER] Problem with loading PDB into tleap Kamali Sripathi (Wed Aug 19 2009 - 08:21:30 CDT)
- [AMBER] why is nonpolar solvation energy not implemented for dynamic in amber TaoPaul (Wed Aug 19 2009 - 10:29:38 CDT)
- [AMBER] ptraj cluster - snapshot number of a representative structure Marcin Krol (Thu Aug 20 2009 - 03:26:09 CDT)
- [AMBER] box volume not understood? Jio M (Thu Aug 20 2009 - 08:54:52 CDT)
- [AMBER] center of mass dhacademic (Thu Aug 20 2009 - 15:50:47 CDT)
- [AMBER] mm_pbsa-Binding and Stability tests? Antonija Tomić (Fri Aug 21 2009 - 05:04:35 CDT)
- [AMBER] update on am1-bcc charge problem in antechamber case (Fri Aug 21 2009 - 11:32:30 CDT)
- [AMBER] PMEMD 10 overflow issues ben rodriguez (Fri Aug 21 2009 - 15:38:05 CDT)
- [AMBER] protein-ligand binding simulation times Andrew Voronkov (Sat Aug 22 2009 - 00:09:54 CDT)
- [AMBER] ambpdb water removal for rst files Andrew Voronkov (Sat Aug 22 2009 - 01:53:14 CDT)
- Re: [AMBER] ambpdb water removal for rst files Bill Ross (Sat Aug 22 2009 - 09:45:30 CDT)
- [AMBER] ptraj-rms vs carnal; questions on RMSD of ligand drift Andrew Voronkov (Sun Aug 23 2009 - 06:55:01 CDT)
- [AMBER] Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Andrew Voronkov (Sun Aug 23 2009 - 08:48:07 CDT)
- [AMBER] acetone lib and frcmod files? Jose Borreguero (Sun Aug 23 2009 - 16:36:43 CDT)
- [AMBER] ABMD Reaction Coordinates stephane acoca (Sun Aug 23 2009 - 22:11:09 CDT)
- [AMBER] ABMD Reaction Coordinates stephane acoca (Sun Aug 23 2009 - 22:24:32 CDT)
- [AMBER] ABMD Reaction Coordinates stephane acoca (Sun Aug 23 2009 - 22:25:43 CDT)
- [AMBER] ABMD Reaction Coordinates stephane acoca (Mon Aug 24 2009 - 00:04:58 CDT)
- [AMBER] Note regarding posting of the same message multiple times Ross Walker (Mon Aug 24 2009 - 00:19:36 CDT)
- [AMBER] Meaning of GMAX E.M. (Mon Aug 24 2009 - 04:05:10 CDT)
- [AMBER] how to add a new atomtype for MM/GB/SA decomposition analysis TaoPaul (Mon Aug 24 2009 - 09:03:51 CDT)
- [AMBER] ptraj limit on trajectory size Sasha Buzko (Mon Aug 24 2009 - 11:59:30 CDT)
- [AMBER] problem compiling amber tools with gcc-4.4.1 gilbert_at_bluemarble.net (Mon Aug 24 2009 - 22:07:44 CDT)
- [AMBER] sander does not print out all residues in range. Maria Mirza (Mon Aug 24 2009 - 23:32:31 CDT)
- [AMBER] NATOM in prmtop and inpcrd files does not agree with the input Maria Mirza (Mon Aug 24 2009 - 23:41:39 CDT)
- [AMBER] ambertools test faied subarna thakur (Tue Aug 25 2009 - 06:01:12 CDT)
- [AMBER] Epsilon value for Iron bharat lakhani (Tue Aug 25 2009 - 07:24:10 CDT)
- [AMBER] Single Adenine ros (Wed Aug 26 2009 - 01:09:23 CDT)
- [AMBER] Chirality error in pdb xiawei (Wed Aug 26 2009 - 02:02:43 CDT)
- [AMBER] ZPVE simple question ondrej.prenosil_at_marge.uochb.cas.cz (Wed Aug 26 2009 - 04:42:04 CDT)
- [AMBER] Need you help bharat lakhani (Wed Aug 26 2009 - 08:41:17 CDT)
- [AMBER] Re: question_on_MMPBSA jackie (Wed Aug 26 2009 - 10:08:01 CDT)
- [AMBER] Inquiries about antechamber Yikan Chen (Wed Aug 26 2009 - 12:07:20 CDT)
- [AMBER] SCC-DFTB MD for mercury ions in proteins Vaida Arciðauskaitë (Thu Aug 27 2009 - 11:41:17 CDT)
- [AMBER] Setting a constrain in one direction Darren Yang (Thu Aug 27 2009 - 22:15:30 CDT)
- [AMBER] Regarding principal component analysis using ptraj Arvind Marathe (Fri Aug 28 2009 - 01:54:40 CDT)
- [AMBER] (no subject) workalemahu berhanu (Fri Aug 28 2009 - 09:06:56 CDT)
- [AMBER] about file format Jia Xu (Sat Aug 29 2009 - 02:55:49 CDT)
- [AMBER] radius for Manganese ion Chunliyan (Sat Aug 29 2009 - 09:43:00 CDT)
- [AMBER] Dyndom Chunliyan (Sat Aug 29 2009 - 09:43:00 CDT)
- [AMBER] (no subject) workalemahu berhanu (Sat Aug 29 2009 - 10:29:34 CDT)
- [AMBER] problem with 4-Hydroxyl-Proline tutorial Jia Xu (Sun Aug 30 2009 - 02:46:18 CDT)
- [AMBER] Changing pH of the system nicholus bhattacharjee (Sun Aug 30 2009 - 06:13:17 CDT)
- [AMBER] How to derive charges from the output bharat lakhani (Mon Aug 31 2009 - 00:33:21 CDT)
- [AMBER] Query regarding watershell command Mannan (Mon Aug 31 2009 - 05:38:08 CDT)
- [AMBER] divcon question Andrei Neamtu (Mon Aug 31 2009 - 06:31:35 CDT)
- [AMBER] ATP/GTP parameters Steve Seibold (Mon Aug 31 2009 - 07:33:04 CDT)
- [AMBER] GTP/ATP parameters Steve Seibold (Mon Aug 31 2009 - 07:44:56 CDT)
- [AMBER] momentum in MD simulation dhacademic (Mon Aug 31 2009 - 09:37:42 CDT)
- [AMBER] antechamber bug report Matthew Walsh (Mon Aug 31 2009 - 11:43:08 CDT)
- [AMBER] Docking with Amber Jordan, Brad (Mon Aug 31 2009 - 15:01:15 CDT)
- [AMBER] ACE and NME patch: VMD ??? Siddharth Rastogi (Mon Aug 31 2009 - 19:25:47 CDT)
- [AMBER] how to pull a dna balaji nagarajan (Mon Aug 31 2009 - 21:39:10 CDT)
Last message date: Thu Dec 31 2009 - 22:57:46 CST
Archived on: Thu Dec 31 2009 - 22:58:33 CST
461 messages sorted by:
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