AMBER Archive (2009) - Oct 2009 By ThreadMost recent messages
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Starting: Thu Oct 01 2009 - 06:31:51 CDT
Ending: Sat Oct 31 2009 - 23:59:38 CDT
- [AMBER] decomposing energies Beroza, Paul (Thu Oct 01 2009 - 11:15:07 CDT)
- [AMBER] Environment Variables in Cygwin Don't Remain Wallace Kunin (Thu Oct 01 2009 - 11:54:29 CDT)
- Re: [AMBER] Environment Variables in Cygwin Don't Remain Bill Ross (Thu Oct 01 2009 - 13:57:43 CDT)
- [AMBER] method used to determine partial charges? Paul Brandt (Thu Oct 01 2009 - 15:25:54 CDT)
- [AMBER] Dipole moment visualization. K.R. (Thu Oct 01 2009 - 16:37:29 CDT)
- [AMBER] red problem James Moore (Thu Oct 01 2009 - 20:52:46 CDT)
- [AMBER] Protein and charged surface rrd (Thu Oct 01 2009 - 22:49:18 CDT)
- [AMBER] Different optimized structures with HF and B3LYP Sanghwa Han (Fri Oct 02 2009 - 02:50:10 CDT)
- [AMBER] MM_PBSA decomposition pair question Rubben Torella (Fri Oct 02 2009 - 06:09:38 CDT)
- [AMBER] minimization error balaji nagarajan (Fri Oct 02 2009 - 06:42:54 CDT)
- [AMBER] Missing X11 Libraries Wallace Kunin (Fri Oct 02 2009 - 11:43:59 CDT)
- [AMBER] RMSD vs time and RMSD vs residues Olotu Odunayo (Fri Oct 02 2009 - 12:40:40 CDT)
- [AMBER] probelm-APBS Rilei Yu (Sat Oct 03 2009 - 00:41:07 CDT)
- [AMBER] MMPBSA: No radius found for F Jeff Yeo (Sun Oct 04 2009 - 19:10:12 CDT)
- [AMBER] TiO2 modeling stefano_elli_at_libero.it (Mon Oct 05 2009 - 11:00:59 CDT)
- [AMBER] R.E.D.-III.3 tools release - q4md-forcefieldtools.org FyD (Sun Oct 04 2009 - 09:37:06 CDT)
- [AMBER] pucker calculation for six member rings Ganesh Kamath (Mon Oct 05 2009 - 13:03:15 CDT)
- [AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out Jeff Yeo (Mon Oct 05 2009 - 18:22:53 CDT)
- [AMBER] MM_PBSA: abnormal VDW interaction energy LIU Huanxiang (Mon Oct 05 2009 - 21:43:21 CDT)
- [AMBER] mm_pbsa- Decomposition: bad atom type Antonija Tomić (Tue Oct 06 2009 - 08:53:25 CDT)
- [AMBER] Problem with memory in nmode analysis Alireza Shaneh (Tue Oct 06 2009 - 10:23:55 CDT)
- [AMBER] using RESP program gunajyoti das (Wed Oct 07 2009 - 05:30:27 CDT)
- [AMBER] Re: Fw: Help required in Amber10 Installation Sudeep Narayan Banerjee (Wed Oct 07 2009 - 10:48:02 CDT)
- Re: [AMBER] Re: Fw: Help required in Amber10 Installation Bill Ross (Wed Oct 07 2009 - 11:59:21 CDT)
- [AMBER] Combine and rename group of residues in xleap Lili Peng (Wed Oct 07 2009 - 16:49:23 CDT)
- [AMBER] The hydrophobic contribution Rilei Yu (Thu Oct 08 2009 - 00:48:32 CDT)
- [AMBER] Fwd: Group specification Pavan G (Thu Oct 08 2009 - 13:30:09 CDT)
- Re: [AMBER] Fwd: Group specification Bill Ross (Thu Oct 08 2009 - 15:15:44 CDT)
- [AMBER] RE: VDW and TI for free energy Ross Walker (Thu Oct 08 2009 - 19:43:48 CDT)
- [AMBER] ff03 parameter for GDP and GTP mmg8_at_ualberta.ca (Thu Oct 08 2009 - 20:05:18 CDT)
- [AMBER] Some queries about pH simulation nicholus bhattacharjee (Thu Oct 08 2009 - 23:36:56 CDT)
- [AMBER] DG improper torsion problem, two missing parameters Youn Kyeung Lee (Fri Oct 09 2009 - 02:02:03 CDT)
- [AMBER] Distance Replica Exchange Steve Seibold (Fri Oct 09 2009 - 08:18:44 CDT)
- Re: [AMBER] DG improper torsion problem, two missing parameters Bill Ross (Fri Oct 09 2009 - 12:25:30 CDT)
- [AMBER] The -c option in Sander phani ghanakota (Fri Oct 09 2009 - 19:47:18 CDT)
- [AMBER] RE: VDW and TI for free energy Qicun Shi (Fri Oct 09 2009 - 21:00:08 CDT)
- [AMBER] decomposition and calculation of entropy Qinghua Liao (Sat Oct 10 2009 - 01:13:49 CDT)
- [AMBER] xleap-does not work Rilei Yu (Sat Oct 10 2009 - 03:30:06 CDT)
- [AMBER] A bug in LEaP ? FyD (Sun Oct 11 2009 - 07:08:37 CDT)
- [AMBER] Energy-from-MM/PBSA-VS-experiment Rilei Yu (Sun Oct 11 2009 - 07:53:00 CDT)
- [AMBER] S-S problem-in protein Rilei Yu (Sun Oct 11 2009 - 20:53:24 CDT)
- [AMBER] unit converter for force constants GÜL ALTINBAŞ (Mon Oct 12 2009 - 07:22:00 CDT)
- [AMBER] unit convertion for force constants GÜL ALTINBAŞ (Mon Oct 12 2009 - 07:47:42 CDT)
- [AMBER] OpenMP Ben Roberts (Mon Oct 12 2009 - 12:35:35 CDT)
- [AMBER] Simulating transmembrane protein. Jayalakshmi Sridhar (Mon Oct 12 2009 - 13:42:11 CDT)
- [AMBER] Is iwrap mapping water molecules to my protein cavity? ben rodriguez (Mon Oct 12 2009 - 13:55:23 CDT)
- Re: [AMBER] Simulating transmembrane protein. Bill Ross (Mon Oct 12 2009 - 14:04:36 CDT)
- Re: [AMBER] Is iwrap mapping water molecules to my protein cavity? Bill Ross (Mon Oct 12 2009 - 14:12:19 CDT)
- [AMBER] Computing an Hessian matrix using NAB Brut Marie (Mon Oct 12 2009 - 17:12:44 CDT)
- [AMBER] How to prepare the acetate ion file in leap? xuemeiwang1103 (Tue Oct 13 2009 - 02:05:57 CDT)
- [AMBER] "Cannot open file ATOMTYPE.INF, exit" when using antechamber haifeng yuan (Tue Oct 13 2009 - 02:44:55 CDT)
- [AMBER] iAPBS - how to set the right grid dimensions Oliver Kuhn (Tue Oct 13 2009 - 03:36:27 CDT)
- [AMBER] LES and NEB problem Rima Chaudhuri (Tue Oct 13 2009 - 14:35:37 CDT)
- [AMBER] mean square displacment Nancy (Tue Oct 13 2009 - 18:59:15 CDT)
- Re: [AMBER] mean square displacment Bill Ross (Tue Oct 13 2009 - 19:09:49 CDT)
- [Amber]AMBER: MM_PBSA problems in AMBER10 He Hongqing (Tue Oct 13 2009 - 22:43:57 CDT)
- [AMBER] How to add a hydrogen to the residue? xuemeiwang1103 (Tue Oct 13 2009 - 22:57:53 CDT)
- Re: Re: 回复: [Amber]AMBER: MM_PBSA problemsin AMBER10 He Hongqing (Wed Oct 14 2009 - 03:39:33 CDT)
- [AMBER] Add the hydrogen to the carboxyl of the GLU residue? xuemeiwang1103 (Wed Oct 14 2009 - 07:05:48 CDT)
- [AMBER] ptraj and prmtop Beale, John (Wed Oct 14 2009 - 07:46:11 CDT)
- [AMBER] six member pucker calculation Ganesh Kamath (Wed Oct 14 2009 - 09:27:24 CDT)
- [AMBER] nab normal mode analysis has imaginary frequencies Junmei Wang (Wed Oct 14 2009 - 11:05:06 CDT)
- [AMBER] installation of Amber on OSX Ramgopal Mettu (Wed Oct 14 2009 - 16:46:59 CDT)
- [AMBER] Simulated annealing waleed zalloum (Thu Oct 15 2009 - 05:59:29 CDT)
- [AMBER] part of the protein escaped from the water box qiaoyan (Thu Oct 15 2009 - 06:33:00 CDT)
- [AMBER] Large File Support Beale, John (Thu Oct 15 2009 - 07:40:27 CDT)
- [AMBER] AMBER 11. Peter Winn (Thu Oct 15 2009 - 11:27:39 CDT)
- [AMBER] B-factor Cristina Sisu (Thu Oct 15 2009 - 12:04:25 CDT)
- [AMBER] cross correlation analysis with ptraj Junmei Wang (Thu Oct 15 2009 - 11:49:29 CDT)
- [AMBER] question with pucker in six member ring Ganesh Kamath (Thu Oct 15 2009 - 14:55:45 CDT)
- [AMBER] why is TAUTP scaled by "e" ? Jose Borreguero (Thu Oct 15 2009 - 15:49:18 CDT)
- [AMBER] eigenvalues add up to more than trace of matrix Yaw Sing TAN (Thu Oct 15 2009 - 22:14:59 CDT)
- [AMBER] How to introduce the second protein molecule into simulation box? Siddharth Rastogi (Fri Oct 16 2009 - 02:00:03 CDT)
- [AMBER] Re: AMBER: periodic bondary condition Markus Kaukonen (Fri Oct 16 2009 - 02:38:03 CDT)
- [AMBER] binding energy Simon Becker (Fri Oct 16 2009 - 04:28:39 CDT)
- [AMBER] MMTSB cluster analysis versus ptraj cluster analysis Cenk \(Jenk\) Andac (Fri Oct 16 2009 - 07:19:24 CDT)
- [AMBER] AMBER FF and NAMD stefano_elli\_at_libero\.it (Fri Oct 16 2009 - 09:26:14 CDT)
- [AMBER] Dihedral energy profile in a single molecule Frank X. Vzquez (Fri Oct 16 2009 - 09:55:53 CDT)
- [AMBER] RDC and alignment tensor Eliana Asciutto (Fri Oct 16 2009 - 15:21:34 CDT)
- [AMBER] (no subject) Prakash Patodia (Sat Oct 17 2009 - 02:12:39 CDT)
- [AMBER] How create PRMTOP and INCPRD for surface? rrd (Sat Oct 17 2009 - 21:40:02 CDT)
- [AMBER] how to get hold of older versions of MKL ? Nahoum Anthony (Mon Oct 19 2009 - 03:59:57 CDT)
- AW: [AMBER] Add the hydrogen to the carboxyl of the GLU residue? Aust, Susanne (Mon Oct 19 2009 - 04:01:27 CDT)
- [AMBER] error message from iAPBS Oliver Kuhn (Mon Oct 19 2009 - 06:47:32 CDT)
- [AMBER] Re: RDC and alignment tensor Eliana Asciutto (Mon Oct 19 2009 - 12:51:50 CDT)
- [AMBER] Centering and reimaging with ptraj- stop rotating. ben rodriguez (Mon Oct 19 2009 - 22:00:26 CDT)
- [AMBER] Error: unable to find mopac charges in mopac.out Rilei Yu (Tue Oct 20 2009 - 00:34:34 CDT)
- [AMBER] How to create FF for diamond. rrd (Tue Oct 20 2009 - 01:16:07 CDT)
- [AMBER] GAFF parameter stefano_elli\_at_libero\.it (Tue Oct 20 2009 - 08:26:26 CDT)
- [AMBER] question with hbond in carnal Ganesh Kamath (Tue Oct 20 2009 - 08:58:36 CDT)
- [AMBER] HBOND analysis Marcin Krol (Tue Oct 20 2009 - 10:42:35 CDT)
- Re: [AMBER] question with hbond in carnal Bill Ross (Tue Oct 20 2009 - 11:32:56 CDT)
- [AMBER] can I run EVB in other ensemble than NVE? Jose Borreguero (Tue Oct 20 2009 - 11:57:04 CDT)
- [AMBER] man pages? Louis-Frdric Feuillette (Tue Oct 20 2009 - 12:09:09 CDT)
- [AMBER] amber8 pmemd trajectory coordinates problem wong105_at_llnl.gov (Tue Oct 20 2009 - 19:32:24 CDT)
- [AMBER] simulation blown up moitrayee_at_mbu.iisc.ernet.in (Tue Oct 20 2009 - 12:41:29 CDT)
- [AMBER] Problem with running anal module in amber moitrayee_at_mbu.iisc.ernet.in (Wed Oct 21 2009 - 01:47:17 CDT)
- [AMBER] "extra points" incompatibility with pmemd mousumi (Wed Oct 21 2009 - 02:57:51 CDT)
- [AMBER] Can I use other ntb options in constant pH simulation nicholus bhattacharjee (Wed Oct 21 2009 - 04:26:43 CDT)
- [AMBER] Why the calculation ofen stop with the calculation process not end? xuemeiwang1103 (Wed Oct 21 2009 - 09:04:57 CDT)
- [AMBER] xleap editing window icons inactive Jayalakshmi Sridhar (Wed Oct 21 2009 - 13:20:01 CDT)
- [AMBER] Circular RNA topology file Kasprzak, Wojciech (NIH/NCI) [C] (Wed Oct 21 2009 - 13:26:04 CDT)
- Re: [AMBER] translate multiple residues Bill Ross (Wed Oct 21 2009 - 15:53:20 CDT)
- [AMBER] Ptraj Segmentation Fault Katrina Hill (Wed Oct 21 2009 - 21:15:31 CDT)
- [AMBER] too many undefined parameters in frcmod xueqin pang (Thu Oct 22 2009 - 03:52:57 CDT)
- [AMBER] units of measures lorenzo (Thu Oct 22 2009 - 06:20:26 CDT)
- [AMBER] problem with minimization moitrayee_at_mbu.iisc.ernet.in (Thu Oct 22 2009 - 06:01:14 CDT)
- [AMBER] [Fwd: problem with minimization] moitrayee_at_mbu.iisc.ernet.in (Thu Oct 22 2009 - 07:46:32 CDT)
- [AMBER] parameters for O2 molecule Jeffrey (Thu Oct 22 2009 - 08:32:07 CDT)
- [AMBER] charges for heme-cys in p450 Jayalakshmi Sridhar (Thu Oct 22 2009 - 11:03:08 CDT)
- [AMBER] Unable to correctly identify element when running QM/MM in amber10 Jifeng Wang (Thu Oct 22 2009 - 11:20:30 CDT)
- Re: [AMBER] [Fwd: problem with minimization] Bill Ross (Thu Oct 22 2009 - 11:49:45 CDT)
- [AMBER] XServe cluster Abdul Rehman Gani (Thu Oct 22 2009 - 14:14:36 CDT)
- [AMBER] Question about distance restraint ? xuemeiwang1103 (Fri Oct 23 2009 - 05:07:47 CDT)
- [AMBER] amber parallel test fail Nahoum Anthony (Fri Oct 23 2009 - 05:20:45 CDT)
- [AMBER] software to hydrate protein pockets Vlad Cojocaru (Fri Oct 23 2009 - 07:23:54 CDT)
- [AMBER] pmemd ifort problem Sel Ercan (Fri Oct 23 2009 - 09:57:59 CDT)
- [AMBER] inhibitor prepin not recognized in xleap Jayalakshmi Sridhar (Fri Oct 23 2009 - 10:56:40 CDT)
- [AMBER] inhibitor prepin not recognized in xleap Jayalakshmi Sridhar (Fri Oct 23 2009 - 11:05:46 CDT)
- [AMBER] xleap not reconizing inhibitor prepin Jayalakshmi Sridhar (Fri Oct 23 2009 - 11:21:07 CDT)
- Re: [AMBER] inhibitor prepin not recognized in xleap Bill Ross (Fri Oct 23 2009 - 13:32:03 CDT)
- Re: [AMBER] xleap not reconizing inhibitor prepin Bill Ross (Fri Oct 23 2009 - 13:33:44 CDT)
- [AMBER] the criterion of equilibrium qiaoyan (Fri Oct 23 2009 - 21:19:58 CDT)
- [AMBER] resp_problem vhakkim boy (Sat Oct 24 2009 - 05:16:22 CDT)
- Re: [AMBER] the criterion of equilibrium Bill Ross (Sat Oct 24 2009 - 12:19:09 CDT)
- [AMBER] A bug in LEaP II ? FyD (Sun Oct 25 2009 - 07:58:36 CDT)
- [AMBER] error in AMBer distance constraint xuemeiwang1103 (Sun Oct 25 2009 - 21:24:09 CDT)
- Re: [AMBER] error in AMBer distance constraint Bill Ross (Sun Oct 25 2009 - 22:03:19 CDT)
- [AMBER] Preparing distance restraints Yunjie Zhao (Mon Oct 26 2009 - 03:44:58 CDT)
- [AMBER] contradictive hydrogen bonds using ptraj Binbin Liu (Mon Oct 26 2009 - 11:42:20 CDT)
- [AMBER] [amber10] atom groups used in torsion constrain Han Zheng (Mon Oct 26 2009 - 13:09:07 CDT)
- [AMBER] PEMD Cristina Sisu (Mon Oct 26 2009 - 16:44:42 CDT)
- [AMBER] Possible bug in "com" group torsion angle constrain? Thanks! Han Zheng (Tue Oct 27 2009 - 12:28:16 CDT)
- [AMBER] NMR restraint xuemeiwang1103 (Tue Oct 27 2009 - 21:31:39 CDT)
- [AMBER] Simulated annealing Shaikh Abdul R S Ramaju (Wed Oct 28 2009 - 00:44:33 CDT)
- [AMBER] Conversion of Gaussian output file to mol2 megha bajaj (Wed Oct 28 2009 - 02:49:51 CDT)
- [AMBER] Conversion of Gaussian output file into mol2 megha bajaj (Wed Oct 28 2009 - 03:00:35 CDT)
- [AMBER] error in distance restraint xuemeiwang1103 (Wed Oct 28 2009 - 08:56:48 CDT)
- [AMBER] pairwise per-residue decomposition manoj singh (Wed Oct 28 2009 - 23:34:32 CDT)
- [AMBER] Thermodynamic Integration calculation on an artificial anion receptor Huifang (Wed Oct 28 2009 - 23:38:05 CDT)
- [AMBER] ligand exiting a protein cavity moitrayee_at_mbu.iisc.ernet.in (Thu Oct 29 2009 - 07:27:58 CDT)
- [AMBER] [Fwd: ligand exiting a protein cavity] moitrayee_at_mbu.iisc.ernet.in (Thu Oct 29 2009 - 07:36:13 CDT)
- [AMBER] rms fit of mutant with respect to wild type structure Siddharth Rastogi (Thu Oct 29 2009 - 08:55:12 CDT)
- [AMBER] Parallel sander & polarisability Thomas Taylor (Thu Oct 29 2009 - 11:19:14 CDT)
- [AMBER] Analyzing per-residue decomposition data manoj singh (Thu Oct 29 2009 - 15:18:45 CDT)
- [AMBER] stacking clusters Shaikh Abdul R S Ramaju (Thu Oct 29 2009 - 21:44:59 CDT)
- [AMBER] some queries on -states flag in constant pH simulation nicholus bhattacharjee (Thu Oct 29 2009 - 23:21:27 CDT)
- [AMBER] Ligand covalent bonds appear to be broken moitrayee_at_mbu.iisc.ernet.in (Fri Oct 30 2009 - 01:32:39 CDT)
- [AMBER] Is it the way to do simulation in vacuum nicholus bhattacharjee (Fri Oct 30 2009 - 05:18:45 CDT)
- [AMBER] SPC/E HOH angle Hemant Kumar (Fri Oct 30 2009 - 05:36:55 CDT)
- [AMBER] RESP charges with -a and without -a flag Jio M (Fri Oct 30 2009 - 08:36:43 CDT)
- [AMBER] Lennard Jones Potential A and B coefficients in Topology file Peter Schmidtke (Fri Oct 30 2009 - 13:32:32 CDT)
- [AMBER] Re: (files attached) RESP with -a and witout -a flag Jio M (Sat Oct 31 2009 - 00:17:55 CDT)
- [AMBER] surface binding protein sadaf iqbal (Sat Oct 31 2009 - 00:28:22 CDT)
- [AMBER] Gaussian log file error megha bajaj (Sat Oct 31 2009 - 08:10:22 CDT)
- Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file Crowley, Michael (Sat Oct 31 2009 - 12:32:12 CDT)
- [AMBER] Different results for different computers cyk5056 (Sat Oct 31 2009 - 14:39:59 CDT)
Last message date: Thu Dec 31 2009 - 22:57:46 CST
Archived on: Thu Dec 31 2009 - 22:58:33 CST
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