Amber Archive Dec 2009 by thread
- Re: [AMBER] distance-dependent dielectric constant minimization Rilei Yu (Mon Nov 30 2009 - 21:31:58 PST)
- Re: [AMBER] Regarding rigid bond aneesh cna (Mon Nov 30 2009 - 21:35:03 PST)
- [AMBER] ptraj utility Neha Bharat Gajaria (Tue Dec 01 2009 - 00:30:07 PST)
- Re: [AMBER] problem with FAD in tleap M. Shahid (Tue Dec 01 2009 - 03:54:04 PST)
- Re: [AMBER] trajout problem Daniel Roe (Tue Dec 01 2009 - 04:34:34 PST)
- RE: [AMBER] trouble with antechamber Jennifer L. Muzyka (Tue Dec 01 2009 - 07:10:40 PST)
- Re: [AMBER] Output Does Not Match in Tutorial B1 Wallace Kunin (Tue Dec 01 2009 - 10:00:48 PST)
- [AMBER] XLEaP Error on Closing Edit Wallace Kunin (Tue Dec 01 2009 - 10:43:27 PST)
- [AMBER] Re: looking for parameters for DHFR substrates and inhibitors... [one more try] Sidney Elmer (Tue Dec 01 2009 - 15:34:36 PST)
- [AMBER] How to get total energy of a system from QM/MM gunajyoti das (Wed Dec 02 2009 - 00:56:06 PST)
- [AMBER] MMGBSA Zhongjie Liang (Wed Dec 02 2009 - 17:17:44 PST)
- [AMBER] look at Amber's slides, email Sally Pias (Wed Dec 02 2009 - 21:08:47 PST)
- [AMBER] Segmentation fault gurunath katagi (Wed Dec 02 2009 - 22:45:20 PST)
- [AMBER] NAB example scripts in AmberTools (Amber 10) Christopher Wassman (Thu Dec 03 2009 - 01:08:37 PST)
- [AMBER] binding energy of multiple ligand-receptor complex 欧阳德方 (Thu Dec 03 2009 - 02:51:17 PST)
- [AMBER] QM/MM input file error mahesh kumar (Thu Dec 03 2009 - 06:05:25 PST)
- [AMBER] semiempirical copper Jacopo Sgrignani (Thu Dec 03 2009 - 06:09:57 PST)
- [AMBER] Comparison of the CHARMM and AMBER parameters for alkane intra\\sa175950 (Thu Dec 03 2009 - 08:49:28 PST)
- [AMBER] AmberTools modifications for Ubuntu 9.10 peker milas (Thu Dec 03 2009 - 13:58:31 PST)
- [AMBER] help with TIP4P and mpi pmemd Hashem Taha (Thu Dec 03 2009 - 14:16:22 PST)
- [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Diego Javier Alonso de Armiño (Thu Dec 03 2009 - 17:47:08 PST)
- [AMBER] sodium ions before or after solvation makes a difference Naser Alijabbari (Thu Dec 03 2009 - 21:01:13 PST)
- Re: [AMBER] Scripting tleap Jio M (Thu Dec 03 2009 - 22:04:01 PST)
- [AMBER] mm_pbsa- Decomposition: bad atom type Antonija Tomić (Fri Dec 04 2009 - 01:27:31 PST)
- [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov (Fri Dec 04 2009 - 01:55:05 PST)
- [AMBER] aromatic ring getting distorted Jio M (Fri Dec 04 2009 - 02:03:49 PST)
- [AMBER] problem with antechamber sculiujl (Fri Dec 04 2009 - 03:38:04 PST)
- [AMBER] COOH group troubling Jio M (Sun Dec 06 2009 - 05:57:06 PST)
- Re: [AMBER] COOH group troubling Bill Ross (Sun Dec 06 2009 - 08:46:58 PST)
- Re: [AMBER] ambpdb water removal for rst files Andrew Voronkov (Sun Dec 06 2009 - 11:44:28 PST)
- [AMBER] how to restart the stopped MM-GBSA job Zhongjie Liang (Sun Dec 06 2009 - 17:36:56 PST)
- [AMBER] Problem of MM-PBSA 欧阳德方 (Sun Dec 06 2009 - 21:09:47 PST)
- [AMBER] force field parameters Piotr Cieplak (Sun Dec 06 2009 - 23:25:03 PST)
- [AMBER] phosphorus to carbon on minimization Alexander Boncheff (Mon Dec 07 2009 - 07:48:45 PST)
- [AMBER] Topology Reorder for EVB Andrea Coletta (Mon Dec 07 2009 - 07:58:50 PST)
- [AMBER] Parametrizing charges for modified DNA bases Bob Johnson (Mon Dec 07 2009 - 10:05:09 PST)
- [AMBER] question about failures peker milas (Mon Dec 07 2009 - 19:37:40 PST)
- [AMBER] myristate to palmitate transformation Anthony Pemberton (Tue Dec 08 2009 - 08:24:59 PST)
- [AMBER] Custom RNA modeling Wallace Kunin (Tue Dec 08 2009 - 12:27:55 PST)
- Re: [AMBER] ptraj image Bill Ross (Tue Dec 08 2009 - 14:08:42 PST)
- [AMBER] Nmode "not running properly" problem in MM_PBSA Du Yun (Tue Dec 08 2009 - 17:56:48 PST)
- [AMBER] PIMD test stalling peker milas (Tue Dec 08 2009 - 18:23:45 PST)
- [AMBER] how to add desired number of water balaji nagarajan (Tue Dec 08 2009 - 19:18:49 PST)
- Re: [AMBER] ATP/GTP parameters E.M. (Tue Dec 08 2009 - 20:36:19 PST)
- [AMBER] ptraj image Neha Bharat Gajaria (Tue Dec 08 2009 - 22:13:36 PST)
- [AMBER] Re: ATP/GTP parameters FyD (Tue Dec 08 2009 - 22:51:03 PST)
- [AMBER] Re: COOH troubling Jio M (Wed Dec 09 2009 - 04:16:17 PST)
- [AMBER] Re: COOH group trouble Jio M (Wed Dec 09 2009 - 08:38:09 PST)
- Re: [AMBER] how to add desired number of water Bill Ross (Wed Dec 09 2009 - 09:46:59 PST)
- Re: [AMBER] ambertools and Snow Leopard 64 bits kernel Scott Brozell (Wed Dec 09 2009 - 13:48:30 PST)
- [AMBER] Re: nab normal mode analysis has imaginary frequencies Junmei Wang (Wed Dec 09 2009 - 15:34:28 PST)
- [AMBER] pressure tensor components Silvia Carlotto (Thu Dec 10 2009 - 05:12:51 PST)
- [AMBER] MMPBSA on a selected region ERIK.LAURINI.phd.units.it (Thu Dec 10 2009 - 10:20:19 PST)
- RE: [AMBER] antechamber error Mike Hanby (Thu Dec 10 2009 - 14:34:30 PST)
- [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide Dongshan Wei (Thu Dec 10 2009 - 15:40:19 PST)
- [AMBER] QM/MM minimization Hashem Taha (Fri Dec 11 2009 - 10:24:25 PST)
- [AMBER] amber10 pmemd fail Aragorn Steiger (Fri Dec 11 2009 - 12:35:49 PST)
- FW: Solvent/solute ratio? Re: [AMBER] how to add desired number of water Hopkins, Robert (Fri Dec 11 2009 - 14:05:51 PST)
- Re: FW: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water Hopkins, Robert (Fri Dec 11 2009 - 14:24:02 PST)
- RE: [Possible Spam: 10%] RE: FW: Solvent/solute ratio? Re: [AMBER] how to add desirednumberof water Hopkins, Robert (Sat Dec 12 2009 - 16:29:04 PST)
- [AMBER] amber.ambermd.org shumao.cqut.edu.cn (Sun Dec 13 2009 - 19:01:18 PST)
- [AMBER] How to run LEaP in a shell file? SongLin (Sun Dec 13 2009 - 23:10:00 PST)
- [AMBER] Different simulation times for similar systems Oliver Kuhn (Mon Dec 14 2009 - 04:31:50 PST)
- [AMBER] how can i include ANP residue Bradley Dickson (Mon Dec 14 2009 - 07:07:50 PST)
- Re: [AMBER] AMBER: segmentation fault when running parmchk Scott Brozell (Mon Dec 14 2009 - 10:14:15 PST)
- [AMBER] Installation on MacOSX Freedman, Tanya (Mon Dec 14 2009 - 10:59:06 PST)
- [AMBER] comparing coordinates from restart file and ptraj outputs Sidney Elmer (Mon Dec 14 2009 - 17:23:50 PST)
- Re: [AMBER] Segmentation fault in antechamber Scott Brozell (Mon Dec 14 2009 - 21:34:39 PST)
- [AMBER] Number of Cycles s. Bill (Tue Dec 15 2009 - 00:31:21 PST)
- [AMBER] addles - neb error balaji nagarajan (Tue Dec 15 2009 - 06:38:53 PST)
- [AMBER] non standard residue and bond command Neha Bharat Gajaria (Wed Dec 16 2009 - 01:50:02 PST)
- [AMBER] chemical shifts: nter and cter Eliana Asciutto (Wed Dec 16 2009 - 11:55:14 PST)
- [AMBER] NAMD dcd files in ptraj Ganesh Kamath (Wed Dec 16 2009 - 13:04:25 PST)
- [AMBER] Parameters for HYP and CGU Rilei Yu (Wed Dec 16 2009 - 19:17:40 PST)
- [AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5 Nils Jan Daniel Drechsel (Thu Dec 17 2009 - 01:52:59 PST)
- [AMBER] what the value of "Br" bondi radii, and how to modify "fillratio" error message. 木野 亮平 (Thu Dec 17 2009 - 01:59:29 PST)
- [AMBER] MM_PBSA Problem (no radius for ion) s. Bill (Thu Dec 17 2009 - 11:39:49 PST)
- [AMBER] Compatibility of ONIOM and Amber vaibhav dixit (Thu Dec 17 2009 - 22:30:32 PST)
- [AMBER] Inorganic Phosphate Parameters Cihan Aydin (Fri Dec 18 2009 - 12:19:21 PST)
- [AMBER] antechamber bond type error Mark M Huntress (Fri Dec 18 2009 - 14:26:57 PST)
- [AMBER] note on Antechamber error Mark M Huntress (Fri Dec 18 2009 - 14:27:50 PST)
- [AMBER] SQM and AMBER Jio M (Fri Dec 18 2009 - 22:36:05 PST)
- [AMBER] Non-Standard Atoms Jack Shultz (Sat Dec 19 2009 - 17:56:28 PST)
- [AMBER] hi ashish pandey (Sun Dec 20 2009 - 22:45:40 PST)
- [AMBER] Sander crash, corrupt rst file... Waqas Nasir (Mon Dec 21 2009 - 03:44:42 PST)
- [AMBER] (No reply) Compatibility of ONIOM and Amber vaibhav dixit (Mon Dec 21 2009 - 05:58:03 PST)
- [AMBER] Release of AmberTools, version 1.3 David A. Case (Mon Dec 21 2009 - 06:33:20 PST)
- [AMBER] Gaff compatible with ff899.SB Pol Boudard (Mon Dec 21 2009 - 07:03:25 PST)
- [AMBER] MM PBSA stats Peter Jones (Mon Dec 21 2009 - 21:57:51 PST)
- [AMBER] PQR file - HELP PLEASE s. Bill (Tue Dec 22 2009 - 04:57:48 PST)
- [AMBER] MMGBSA error Zhongjie Liang (Tue Dec 22 2009 - 05:04:09 PST)
- [AMBER] sqm x mopac in AmberTools 1.3 Alan (Tue Dec 22 2009 - 07:02:22 PST)
- [AMBER] Van der Waals and electrostatic Forces Frank X. Vázquez (Tue Dec 22 2009 - 09:42:33 PST)
- [AMBER] HOW TO OPTIMISE INDI-DIELC_MM VALUE for MM_PBSA calculation ? Marek Maly (Tue Dec 22 2009 - 10:49:42 PST)
- [AMBER] pupil and amber davide branduardi (Tue Dec 22 2009 - 12:29:37 PST)
- [AMBER] atom type shamoon siddiqui (Tue Dec 22 2009 - 21:31:42 PST)
- [AMBER] AmberTools-1.3 not compiling on MacOsX Cesar Millan (Tue Dec 22 2009 - 22:37:37 PST)
- [AMBER] typo in AmberTools.pdf (release 1.3) Alan (Wed Dec 23 2009 - 01:51:01 PST)
- [AMBER] using sqm from AmberTools 1.3 Alan (Wed Dec 23 2009 - 02:35:33 PST)
- [AMBER] NEB-error balaji nagarajan (Wed Dec 23 2009 - 08:04:46 PST)
- [AMBER] CHARMM psf file to Amber prmtop file Sarvin Moghaddam (Wed Dec 23 2009 - 08:20:30 PST)
- [AMBER] iron in prepi file generation for heme Donald Keidel (Wed Dec 23 2009 - 14:27:10 PST)
- [AMBER] Adding single distance restraint Adler, Marc (Wed Dec 23 2009 - 18:00:35 PST)
- [AMBER] SQM and AMBER :again Jio M (Wed Dec 23 2009 - 21:18:37 PST)
- [AMBER] OE and CG types Jio M (Thu Dec 24 2009 - 01:26:43 PST)
- [AMBER] implicit solvent MD with fixed residues Hakan Gunaydin (Thu Dec 24 2009 - 15:43:13 PST)
- [AMBER] RE: Amber question Ross Walker (Thu Dec 24 2009 - 15:44:54 PST)
- [AMBER] a problem in building oligosaccharides using LEaP Song Lin (Thu Dec 24 2009 - 18:12:10 PST)
- [AMBER] MMGBSA error Zhongjie Liang (Thu Dec 24 2009 - 22:59:16 PST)
- [AMBER] FW: how to change velocities balaji nagarajan (Fri Dec 25 2009 - 02:23:57 PST)
- [AMBER] a question about ptraj qiaoyan (Fri Dec 25 2009 - 05:58:44 PST)
- [AMBER] PQR files s. Bill (Fri Dec 25 2009 - 06:38:36 PST)
- [AMBER] heating system in NEB balaji nagarajan (Sat Dec 26 2009 - 03:29:35 PST)
- [AMBER] reg.changing velocity balaji nagarajan (Sat Dec 26 2009 - 10:47:10 PST)
- [AMBER] neb error while heating balaji nagarajan (Sat Dec 26 2009 - 19:09:00 PST)
- [AMBER] .rst file error ZhaoLei (Sun Dec 27 2009 - 06:46:37 PST)
- [AMBER] coarse grained Francesco Pietra (Sun Dec 27 2009 - 12:36:02 PST)
- [AMBER] ERROR: Could not read coords from {filename} Paul Brandt (Sun Dec 27 2009 - 20:14:50 PST)
- [AMBER] problem in installing amber tools on Mac OSX 10.6 Chun-Wei Pao (Sun Dec 27 2009 - 23:54:26 PST)
- [AMBER] About APBS radiopt Youn Kyeung Lee (Mon Dec 28 2009 - 02:12:07 PST)
- [AMBER] NEB-NAN error balaji nagarajan (Mon Dec 28 2009 - 07:16:43 PST)
- [AMBER] mpirun error Vijay Manickam Achari (Mon Dec 28 2009 - 19:00:11 PST)
- [AMBER] nab installation Lixia Jin Day (Tue Dec 29 2009 - 09:32:37 PST)
- [AMBER] can I install amber11 on a windowsPC under cygwin? Lixia Jin Day (Tue Dec 29 2009 - 10:06:30 PST)
- [AMBER] sleap in AmberTools 1.3 is not working anymore for me Alan (Tue Dec 29 2009 - 12:27:57 PST)
- [AMBER] Tests to check for proper MMPBSA.py installation RANAJIT SHINDE (Wed Dec 30 2009 - 04:15:48 PST)
- [AMBER] exchange attempt in REMD zgong.hust (Wed Dec 30 2009 - 18:34:21 PST)
- [AMBER] Zinc parameters? xuemeiwang1103 (Wed Dec 30 2009 - 19:37:21 PST)
- [AMBER] hbond analysis qiaoyan (Thu Dec 31 2009 - 00:40:22 PST)
- Last message date: Thu Dec 31 2009 - 18:30:03 PST
- Archived on: Wed Apr 17 2024 - 05:53:50 PDT
