Amber Archive Mar 2014: by messages with attachments

[AMBER] pmemd.cuda segfaults pavel.banas.upol.cz (Mon Mar 03 2014 - 08:09:38 PST)
1. error_massage.txt (17704 bytes)
[AMBER] format of FINAL_DECOMP_MMPBSA.dat Nitin Sharma (Mon Mar 03 2014 - 08:29:00 PST)
1. decompositon_1.jpg (311938 bytes)
2. decompositon_2.jpg (125488 bytes)
3. decompositon_tutorial.jpg (93170 bytes)
Re: [AMBER] Unable to restrain A-DNA conformation DEBOSTUTI GHOSHDASTIDAR (Wed Mar 05 2014 - 05:48:48 PST)
1. ADNA_leap.png (44704 bytes)
[AMBER] Trouble obtaining force field parameters via Antechamber Hyun-seok Kim (Wed Mar 05 2014 - 10:43:49 PST)
1. EC_3.pdb (866 bytes)
[AMBER] Modified RNA frcmod error Sorensen, Jesper (Fri Mar 07 2014 - 16:51:49 PST)
1. all_modrna08.frcmod (79858 bytes)
Re: [AMBER] problem in "re-image" and "unwarp" Vijay Manickam Achari (Mon Mar 10 2014 - 23:37:38 PDT)
1. mol-get-bigger.png (7556 bytes)
[AMBER] pmf -Equilibration termination Rasha Alqus (Mon Mar 17 2014 - 05:25:04 PDT)
1. eq3.out (33831 bytes)
2. eq2.job.e373706 (22730 bytes)
[AMBER] generating topology Vijay Manickam Achari (Wed Mar 19 2014 - 06:47:05 PDT)
1. tryptofanC0.pdb (2270 bytes)
Re: [AMBER] Antechamber not converting HyperChem .hin files correctly David A Case (Thu Mar 20 2014 - 11:25:40 PDT)
1. hin.patch (784 bytes)
[AMBER] Problem with Decomposition of Binding Free Energy loue chen (Sun Mar 23 2014 - 20:31:25 PDT)
1. 03d29dee3a12d0e63885b3e08529208f8c4b6462d875c2dd7f3ccf3d015bd5fb-V_1_.jpg (154591 bytes)
Re: [AMBER] tleap cannot handle dummies in the middle? Hannes Loeffler (Tue Mar 25 2014 - 07:32:27 PDT)
1. pert1.leap (150 bytes)
2. MORPH1.frcmod (903 bytes)
[AMBER] Problem in configuring the amber Akashdeep Biswas (Tue Mar 25 2014 - 23:55:59 PDT)
1. 03-25_17:47:53.png (249027 bytes)
[AMBER] setangle in parmed API hannes.loeffler.stfc.ac.uk (Wed Mar 26 2014 - 08:01:11 PDT)
1. test.parm7 (12248 bytes)
2. test_angle.py (877 bytes)
3. mod.parm7 (7002 bytes)
Re: [AMBER] combining trajectories with diff. number of residues for same protein Nitin Sharma (Thu Mar 27 2014 - 20:13:57 PDT)
1. strip2merge_1.out (2183 bytes)
2. strip2merge_2.out (2266 bytes)
[AMBER] Problem regarding running job in AMBER 12 Souvik Sur (Sat Mar 29 2014 - 04:16:29 PDT)
1. wat_density.in (321 bytes)
2. wat_eq.in (259 bytes)
3. wat_heat1.in (324 bytes)
4. wat_heat2.in (325 bytes)
5. wat_heat3.in (326 bytes)
6. wat_heat4.in (327 bytes)
7. wat_md.in (270 bytes)
8. wat_min1.in (170 bytes)
9. wat_min2.in (130 bytes)
[AMBER] central atom always 3rd in improper Hannes Loeffler (Mon Mar 31 2014 - 07:45:21 PDT)
1. improper.tar.gz (3383 bytes)

Amber Archive Mar 2014 by messages with attachments