Amber Archive Jan 2012: by messages with attachments

[AMBER] Using antechamber -Heme molecule יוכבד (Mon Jan 02 2012 - 03:24:26 PST)
1. NewHeme_gaff.prep (6277 bytes)
Re: [AMBER] how to set the dist.RST file in SMD using Amber11? Adrian Roitberg (Tue Jan 03 2012 - 17:50:50 PST)
1. dist.RST.orig (1496 bytes)
Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu (Wed Jan 04 2012 - 00:07:08 PST)
1. calib.xml (8688 bytes)
2. UNK.log (110756 bytes)
Re: [AMBER] chamber-fortran runtime error colvin (Wed Jan 04 2012 - 01:23:45 PST)
1. fail.psf (2525 bytes)
2. pass.psf (2531 bytes)
[AMBER] ptaj: RMSD George Tzotzos (Wed Jan 04 2012 - 10:15:38 PST)
1. 1.tiff (112344 bytes)
[AMBER] Problem with generating topology file using tleap Devlina Chakravarty (Thu Jan 05 2012 - 00:19:14 PST)
1. leap-error.txt (1101 bytes)
2. H.pdb (145456 bytes)
Re: [AMBER] ptaj: RMSD George Tzotzos (Fri Jan 06 2012 - 10:15:16 PST)
1. 1.tiff (86264 bytes)
[AMBER] system breaks during simulation moitrayee.mbu.iisc.ernet.in (Sat Jan 07 2012 - 11:20:16 PST)
1. rmsd.tif (54334 bytes)
[AMBER] Calculate the cosine content of PC surasak chunsrivirot (Mon Jan 16 2012 - 02:44:20 PST)
1. content.png (5710 bytes)
[AMBER] Problem regarding Molecular Dynamics simulation of DNA using Parmbsc0 and ff99sb Muhammad Khaled Tumbi (Tue Jan 17 2012 - 05:12:51 PST)
1. QNF_ff99sb.png (46253 bytes)
2. QJF_ff99bsc0.png (73137 bytes)
3. QJF_ff99bsc0.png (73137 bytes)
4. QNF_ff99sb.png (46253 bytes)
5. density.in (228 bytes)
6. 1.in (188 bytes)
7. heat.in (361 bytes)
8. min1.in (200 bytes)
9. min2.in (158 bytes)
10. production.in (188 bytes)
[AMBER] Minimization problem for a homotrimer of small molecules Baptiste Legrand (Wed Jan 18 2012 - 03:22:36 PST)
1. min.in (127 bytes)
2. trimer.inpcrd (10740 bytes)
3. trimer.out (195 bytes)
4. trimer.prmtop (119854 bytes)
[AMBER] Adjusting density Beale, John (Wed Jan 18 2012 - 05:28:31 PST)
1. image001.jpg (23871 bytes)
Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Fri Jan 20 2012 - 10:17:11 PST)
1. config.h (4668 bytes)
[AMBER] MCPB: error Pls help kanika singal (Sat Jan 21 2012 - 02:18:56 PST)
1. 1fx7_ms2_fixed.pdb (144180 bytes)
2. 1fx7_ms2_settings.bcl (494 bytes)
3. 1fx7_ms2_sidechain.bcl (3269 bytes)
4. 1fx7_ms2_sidechain.bcl.log (534605 bytes)
Re: [AMBER] MCPB: error Pls help Ben Roberts (Mon Jan 23 2012 - 12:06:32 PST)
1. smime.p7s (2595 bytes)
Re: [AMBER] AmberTools 1.5 & Centos6 Irene Newhouse (Tue Jan 24 2012 - 09:22:21 PST)
1. Makefile (6259 bytes)
Re: [AMBER] AmberTools 1.5 & Centos6 Irene Newhouse (Tue Jan 24 2012 - 11:24:34 PST)
1. Makefile (17292 bytes)
Re: [AMBER] AmberTools 1.5 & Centos6 Irene Newhouse (Tue Jan 24 2012 - 12:01:52 PST)
1. parmSet.c (82828 bytes)
Re: [AMBER] Steered Molecular Dynamics: some questions Dwight McGee (Tue Jan 24 2012 - 18:06:57 PST)
1. dist.RST.nfv.mut.orig (1488 bytes)
[AMBER] peptide+sugar Urszula Uciechowska (Wed Jan 25 2012 - 04:44:51 PST)
1. pep1_sugar_oH.pdb (8257 bytes)
Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Thu Jan 26 2012 - 04:03:22 PST)
1. config.h (4991 bytes)
[AMBER] makeDIST_RST command problem Olena Dobrovolska (Thu Jan 26 2012 - 08:39:05 PST)
1. gcg_b.amb.pdb (90339 bytes)
[AMBER] Splitting cyclic molecule into QM and MM parts Dmitry Nilov (Fri Jan 27 2012 - 05:12:33 PST)
1. qmmm.GIF (3804 bytes)
[AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." Jan-Philip Gehrcke (Fri Jan 27 2012 - 05:51:27 PST)
1. rest (1977 bytes)
2. sander_restraint_parse_testcase.tar.gz (477420 bytes)
Re: [AMBER] makeDIST_RST command problem Olena Dobrovolska (Fri Jan 27 2012 - 06:00:55 PST)
1. 16b_1_12_2.dist (29193 bytes)
2. gcg_b1.amb.pdb (90338 bytes)
3. sign.sed (57 bytes)
Re: [AMBER] makeDIST_RST command problem Olena Dobrovolska (Mon Jan 30 2012 - 08:59:55 PST)
1. 16b_1_12_2.dist (29193 bytes)
2. gcg_b.amb.pdb (90338 bytes)
Re: [AMBER] NMODE list index out of range error Sangeetha B (Mon Jan 30 2012 - 20:26:18 PST)
1. _MMPBSA_ligand_nm.out (58077 bytes)
Re: [AMBER] makeDIST_RST command problem Olena Dobrovolska (Tue Jan 31 2012 - 07:33:09 PST)
1. 16b_1_12_2.dist (29193 bytes)
2. gcg_b.amb.pdb (90338 bytes)
[AMBER] SMD: Segmentation fault George Tzotzos (Tue Jan 31 2012 - 10:32:28 PST)
1. smd.out (9322 bytes)
2. dist.RST (323 bytes)

Amber Archive Jan 2012 by messages with attachments