Amber Archive Mar 2013: by messages with attachments

Re: [AMBER] how to restart a molecular dynamics simulation Hector A. Baldoni (Tue Mar 05 2013 - 12:22:49 PST)
1. JOB.N (836 bytes)
2. prod_N.in (344 bytes)
[AMBER] MMPBSA jobs on a cluster Calcerror: Vivek Shankar Bharadwaj (Wed Mar 06 2013 - 12:05:01 PST)
1. MIO_script_MD (1819 bytes)
2. mmpbsa.in (252 bytes)
[AMBER] Error in MMPBSA Saugata Hazra (Wed Mar 06 2013 - 12:30:00 PST)
1. mmpbsa.in (188 bytes)
Re: [AMBER] MMPBSA jobs on a cluster Calcerror: Vivek Shankar Bharadwaj (Wed Mar 06 2013 - 12:36:30 PST)
1. _MMPBSA_complex_pb.mdout.0 (578651 bytes)
[AMBER] VLIMIT problem with Folic acid (gaff parm) HIMANSHU JOSHI (Wed Mar 06 2013 - 21:19:07 PST)
1. fol_wat.prmtop (496683 bytes)
Re: [AMBER] Number Excluded Atoms List Generation Jason Swails (Thu Mar 07 2013 - 10:52:41 PST)
1. prmtop.pdf (132257 bytes)
[AMBER] Fwd: failed to run sander .... Shashidhar Rao (Thu Mar 07 2013 - 11:13:58 PST)
1. min.out (4904 bytes)
2. min.in (118 bytes)
Re: [AMBER] antechamber dCTP YZ Qin (Fri Mar 08 2013 - 08:01:32 PST)
1. dCTP2.off (6048 bytes)
2. Ternary3.pdb (258874 bytes)
[AMBER] ligand molecule problem tianchuan881 (Sun Mar 10 2013 - 20:08:09 PDT)
1. ligand.frcmod (1368 bytes)
2. ligand.mol2 (4121 bytes)
3. R.pdb (313140 bytes)
Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme Vaibhav Dixit (Sun Mar 10 2013 - 21:37:45 PDT)
1. 2VN0_heme2.pdb (593155 bytes)
2. Heme.mol2 (7844 bytes)
3. Heme.frcmod (1867 bytes)
Re: [AMBER] Regarding centering a tetrameric molecule dilrajl.bii.a-star.edu.sg (Sun Mar 10 2013 - 23:50:16 PDT)
1. 1.png__size_372016 (372016 bytes)
2. 2.png__size_333435 (333435 bytes)
Re: [AMBER] RESP charges for iron-sulfur cluster safwat abdel-azeim (Mon Mar 11 2013 - 04:57:59 PDT)
1. isph_QM_ESP.xyz (2182 bytes)
Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme Vaibhav Dixit (Mon Mar 11 2013 - 08:24:57 PDT)
1. 2VN0_heme2.pdb (592049 bytes)
[AMBER] frcmod file problem tianchuan881 (Tue Mar 12 2013 - 06:09:22 PDT)
1. S.frcmod (1368 bytes)
[AMBER] Problem in parallel installation of Amber 12 Kshatresh Dutta Dubey (Tue Mar 12 2013 - 08:41:49 PDT)
1. log (72541 bytes)
2. install_errors.log (11125 bytes)
Re: [AMBER] Bad atom type: fe in MMPBSA calculations siddharth kesharwani (Thu Mar 14 2013 - 02:18:30 PDT)
1. mdread.f (114144 bytes)
[AMBER] the protein was crashed 纪晓峰 (Fri Mar 15 2013 - 00:44:55 PDT)
1. md.png (131555 bytes)
Re: [AMBER] PMEMD in amber12 Mary Varughese (Mon Mar 18 2013 - 10:58:36 PDT)
1. TbNrb_md9.out (141964 bytes)
Re: [AMBER] Hydration Free Enery by TI Kepa K. Burusco (Tue Mar 19 2013 - 12:27:18 PDT)
1. anq.lib.txt (2457 bytes)
2. anqBOX.pd.txt (139317 bytes)
3. anqWAT.pdb.txt (140125 bytes)
Re: [AMBER] problem combining trajectories with diff. number of residues Vaibhav Dixit (Wed Mar 20 2013 - 22:07:03 PDT)
1. 1FM9_FGZ_VAC.pdb (306423 bytes)
2. 1PRG_VAC.pdb (294875 bytes)
[AMBER] one sided connection warning HEM P450 MD input files Vaibhav Dixit (Sat Mar 23 2013 - 22:53:15 PDT)
1. 2vn0_heme.png (605263 bytes)
[AMBER] patching unsuccessful even after modifying patch_amber.py Vaibhav Dixit (Sun Mar 24 2013 - 05:17:50 PDT)
1. patch_amber.py (42942 bytes)
[AMBER] problem in running antechamber Anshuman Dixit (Tue Mar 26 2013 - 00:39:08 PDT)
1. TTD_f.pdb (5378 bytes)
[AMBER] problem in generating pbsa.phi file using PBSA N Nandi (Thu Mar 28 2013 - 22:06:09 PDT)
1. nuc.rst (310368 bytes)

Amber Archive Mar 2013 by messages with attachments