Amber Archive Dec 2011: by messages with attachments

[AMBER] error in MD simulation kureeckal ramesh (Wed Nov 30 2011 - 19:42:29 PST)
1. equil1.rst (211656 bytes)
[AMBER] atom types error Urszula Uciechowska (Thu Dec 01 2011 - 03:36:06 PST)
1. THS_sm.mol2 (1849 bytes)
Re: [AMBER] atom types error Urszula Uciechowska (Thu Dec 01 2011 - 05:25:32 PST)
1. THS_sm.mol2 (1849 bytes)
Re: [AMBER] CUDA NaN error occuring at "wrapping first mol" Bill Sinko (Thu Dec 01 2011 - 16:20:30 PST)
1. bugfix_log.txt (23383 bytes)
2. 12-01_15-12-16.diff (988 bytes)
3. bugfix_log.txt (23383 bytes)
4. configure.rej (11438 bytes)
5. md_2.out (34599 bytes)
6. nvt.in (513 bytes)
Re: [AMBER] constant pressure kirtana S (Sun Dec 04 2011 - 11:52:54 PST)
1. heat1.dat (15692 bytes)
2. heat2.dat (15692 bytes)
3. heat3.dat (8681 bytes)
4. min1.dat (11417 bytes)
5. min2.dat (10656 bytes)
6. min3.dat (10048 bytes)
[AMBER] Problem with running antechamber on a small molecule Devlina Chakravarty (Mon Dec 05 2011 - 02:53:36 PST)
1. mopac.out (8469 bytes)
2. H-prodrg.pdb (4051 bytes)
[AMBER] atom types for pyridine ... Urszula Uciechowska (Mon Dec 05 2011 - 03:28:09 PST)
1. Mol_sm.mol2 (2161 bytes)
Re: [AMBER] atom types for pyridine ... Urszula Uciechowska (Tue Dec 06 2011 - 02:04:57 PST)
1. PYA.mol2 (2161 bytes)
Re: [AMBER] compiling pmemd in amber9 Vijay Manickam Achari (Tue Dec 06 2011 - 02:50:37 PST)
1. config.h (1242 bytes)
[AMBER] How to turn off non-bonded interactions between non-bonded atoms? Marc van der Kamp (Tue Dec 06 2011 - 08:15:41 PST)
1. 4ions.prmtop (7521 bytes)
2. 4ions_ex.prmtop (7588 bytes)
3. min.log (13732 bytes)
4. min_ex.log (13732 bytes)
Re: [AMBER] MCPB execution error Ben Roberts (Tue Dec 06 2011 - 08:53:36 PST)
1. smime.p7s (4373 bytes)
Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms? Marc van der Kamp (Tue Dec 06 2011 - 12:35:04 PST)
1. 4ions.prmtop (7521 bytes)
2. addexclusions.out (1764 bytes)
3. exclusions2.prmtop (2610 bytes)
Re: [AMBER] MCPB execution error Soma Ghosh (Tue Dec 06 2011 - 22:23:31 PST)
1. 1AMP_OH_sidechain.bcl.log (6591 bytes)
2. config.log (75751 bytes)
Re: [AMBER] atom types for pyridine II... Urszula Uciechowska (Wed Dec 07 2011 - 01:46:06 PST)
1. PYA.mol2 (2161 bytes)
Re: [AMBER] TI in Amber and the TUTORIAL A9 Marek Maly (Thu Dec 08 2011 - 13:48:18 PST)
1. TI.ppt (86016 bytes)
[AMBER] problems with getting right parameters ... Urszula Uciechowska (Fri Dec 09 2011 - 03:58:59 PST)
1. SUN_am.params (178 bytes)
2. SUN_am.mol2 (3223 bytes)
3. SUN.mol2 (2705 bytes)
Re: [AMBER] MCPB execution error Ben Roberts (Sun Dec 11 2011 - 20:12:14 PST)
1. smime.p7s (2595 bytes)
Re: [AMBER] MCPB execution error Ben Roberts (Sun Dec 11 2011 - 20:17:10 PST)
1. smime.p7s (2595 bytes)
[AMBER] The charge is wrong when the ligand together with the large model in MCPB JiYuan Liu (Mon Dec 12 2011 - 22:51:12 PST)
1. 3H68_OH_chg2.prep (11958 bytes)
2. min.in (112 bytes)
3. 3H68_OH_mcpb_min.pdb (406960 bytes)
4. 3H68_OH_mcpb.pdb (396847 bytes)
[AMBER] sourcing solvents.cmd quits xleap/tleap Jio M (Thu Dec 15 2011 - 23:24:59 PST)
1. TP3.pdb (209 bytes)
[AMBER] segmentation fault using GPUs Ouaray Z. (Fri Dec 16 2011 - 03:38:36 PST)
1. leap.in (374 bytes)
2. Val51Min2.in (122 bytes)
3. MutChang_MD.out (9546 bytes)
4. mdrun.in (353 bytes)
[AMBER] Phosphotyrosine connectivity problem Sangeetha B (Mon Dec 19 2011 - 00:41:42 PST)
1. ptr_min2.png (123275 bytes)
Re: [AMBER] Prepping PDB files for amber Jan-Philip Gehrcke (Mon Dec 19 2011 - 15:18:51 PST)
1. cyscyx.sh (1451 bytes)
2. cyslist.sh (954 bytes)
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Tue Dec 20 2011 - 02:03:05 PST)
1. mdout.nvt.SPDP (124169 bytes)
2. mdout.npt.SPDP (156601 bytes)
3. mdout.npt.cpu (162724 bytes)
4. mdout.nvt.cpu (130292 bytes)
Re: [AMBER] MTK++ and MCPB patch released JiYuan Liu (Tue Dec 20 2011 - 05:04:37 PST)
1. 3H68_OH_resNames.bcl (496 bytes)
2. 3H68_OH_settings.bcl (490 bytes)
3. 3H68_OH_params_fc_md.xml (7159 bytes)
4. 3H68_OH_chg2.xml (118646 bytes)
5. 3H68_OH_stdMol.xml (118858 bytes)
6. 3H68_OH_fixed_H.pdb (396840 bytes)
[AMBER] ptraj: Hbonds George Tzotzos (Tue Dec 20 2011 - 09:38:10 PST)
1. analyse_hbond.out (5373 bytes)
Re: [AMBER] MTK++ and MCPB patch released JiYuan Liu (Tue Dec 20 2011 - 18:24:32 PST)
1. caparm.xml (256 bytes)
2. calib.xml (8691 bytes)
[AMBER] problems of results of decomposition Qinghua Liao (Thu Dec 22 2011 - 02:16:02 PST)
1. decomp.png (32671 bytes)
Re: [AMBER] MTK++ and MCPB patch released Martin Peters (Thu Dec 22 2011 - 02:38:06 PST)
1. 3H68_OH.pml (1341 bytes)
2. 3H68_OH.leaprc (633 bytes)
3. 3H68_OH_resNames.bcl.log (40580 bytes)
4. 3H68_OH_mcpb.pdb (396848 bytes)
Re: [AMBER] MTK++ and MCPB patch released JiYuan Liu (Thu Dec 22 2011 - 06:06:19 PST)
1. min.in (112 bytes)
[AMBER] problem with charge on iron in heme cysteine system pancham lal gupta (Thu Dec 22 2011 - 23:57:26 PST)
1. hemopt.log (438524 bytes)
2. hemopt_resp_at.ac (9648 bytes)
Re: [AMBER] cpptraj -- doesn't like reading Amber restart files with more than 99, 999 atoms Daniel Roe (Fri Dec 23 2011 - 09:46:15 PST)
1. bugfix.26 (1362 bytes)
[AMBER] Error in output file Aditya Padhi (Sun Dec 25 2011 - 23:02:38 PST)
1. prod2.out (3168 bytes)

Amber Archive Dec 2011 by messages with attachments