Amber Archive May 2016: by messages with attachments

[AMBER] Ewald force using debugf Zhenyu Meng (Mon May 02 2016 - 04:07:17 PDT)
1. debug.in (378 bytes)
[AMBER] iwrap=1 issue Hirdesh Kumar (Mon May 02 2016 - 04:57:07 PDT)
1. error.png (281635 bytes)
[AMBER] rdf cpptraj. Saman Yousuf ali (Tue May 03 2016 - 02:37:48 PDT)
1. rdf.png (29086 bytes)
Re: [AMBER] tleap - protein + ligand + heme group Anna Cebrian Prats (Tue May 03 2016 - 02:47:55 PDT)
1. def.pdb (359149 bytes)
2. paper.in (4403 bytes)
3. tosco.frcmod (3661 bytes)
4. heme.frcmod (2887 bytes)
5. all-atom.prep (7010 bytes)
[AMBER] process_mdout.perl script Ruth Helena Tichauer (Tue May 03 2016 - 06:35:47 PDT)
1. process_mdout.perl (6098 bytes)
2. summary.DENSITY (1501 bytes)
Re: [AMBER] Ewald force using debugf Zhenyu Meng (Tue May 03 2016 - 20:28:42 PDT)
1. forcedump1.dat (6345 bytes)
2. forcedump2.dat (6345 bytes)
3. ELECTRO3.dat (962 bytes)
4. debug1.in (378 bytes)
5. debug2.in (389 bytes)
Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber Karl Kirschner (Wed May 04 2016 - 01:28:34 PDT)
1. bcc_charges.png (68955 bytes)
2. ca-oh-ho.pdf (6103 bytes)
3. ca-n-c.pdf (6179 bytes)
Re: [AMBER] bad data error in sander run Mary Varughese (Wed May 04 2016 - 05:11:09 PDT)
1. cgc_gens_md2.out (50153 bytes)
2. cgc_gens_md3.out (47809 bytes)
3. cgc_gens_md4.out (51212 bytes)
[AMBER] xLeap Ramkumar B (Thu May 05 2016 - 00:20:55 PDT)
1. test.pdb (59615 bytes)
Re: [AMBER] Restrain a single atom in the residue during minimization, instead of all the atoms in a residue with RES option Vasantha Kumar (Tue May 10 2016 - 01:32:54 PDT)
1. Petide_solvate_min2.out (5926 bytes)
Re: [AMBER] MMPBSA doubt Mary Varughese (Wed May 11 2016 - 21:26:46 PDT)
1. statistics_PB.out (1535 bytes)
2. statistics_PB.out.snap (88494 bytes)
3. statistics_TS.out (945 bytes)
4. statistics_TS.out.snap (44274 bytes)
[AMBER] Unable to run Antechamber Shreeramesh (Fri May 13 2016 - 05:12:48 PDT)
1. lig.mol2 (2805 bytes)
[AMBER] problem with new residu in Xleap Muriel Jourdan (Tue May 17 2016 - 07:15:10 PDT)
1. glydprofluo.inpcrd (10487 bytes)
2. glydprofluo.prmtop (128173 bytes)
[AMBER] QM/MM energy minimization Stanislav Simko (Fri May 20 2016 - 03:34:28 PDT)
1. prmtopbox (8980 bytes)
[AMBER] Problems with GTX titan-X GPU Elvis Martis (Sat May 21 2016 - 03:19:54 PDT)
1. smi.txt (1312 bytes)
2. nvidia.log (5732 bytes)
3. cpu.log (597 bytes)
Re: [AMBER] QM/MM Interface Stanislav Simko (Sun May 22 2016 - 02:31:58 PDT)
1. sub.sh (357 bytes)
Re: [AMBER] QM/MM Interface Nisler, Collin R. (Sun May 22 2016 - 16:46:39 PDT)
1. Capture.PNG (12344 bytes)
Re: [AMBER] Problems with GTX titan-X GPU Elvis Martis (Tue May 24 2016 - 05:20:13 PDT)
1. GPU.large_0.log (850 bytes)
2. GPU_0.log (850 bytes)
3. run_test.log (1347 bytes)
[AMBER] Regarding parameter file not saved Vishal Nemaysh (Tue May 24 2016 - 09:21:10 PDT)
1. neelamber.pdb (225982 bytes)
[AMBER] adaptive qm/mm NVT not reaching target temperature Stanislav Simko (Wed May 25 2016 - 05:58:39 PDT)
1. nvt_fullMM.eps (98930 bytes)
2. temperature0.75.eps (27050 bytes)
Re: [AMBER] CUDA MPI issues Biplab Ghosh (Wed May 25 2016 - 23:00:53 PDT)
1. smi-q.txt (11959 bytes)
2. GPU.large_0.log (850 bytes)
3. GPU.large_1.log (850 bytes)
4. GPU_0.log (850 bytes)
5. GPU_1.log (850 bytes)
6. run_test_biplab.log (1843 bytes)
7. 05-24_16-51-23.diff (62995 bytes)
8. 05-24_16-51-23.log (21724 bytes)
9. pmemd.cuda.MPI.err (2813 bytes)
Re: [AMBER] CUDA MPI issues Biplab Ghosh (Thu May 26 2016 - 11:12:18 PDT)
1. 2.png (77487 bytes)
2. 1.png (33428 bytes)
[AMBER] calculating binding free energy Carlos Romero (Thu May 26 2016 - 17:18:56 PDT)
1. ligando_en_posicion_original.png (7711 bytes)
2. ligando_disperso.png (4988 bytes)
[AMBER] Adaptively Biased MD: Problems with executing groupfile Jason Imamoto (Fri May 27 2016 - 10:20:07 PDT)
1. rs2_1DvA2.groupfile (555 bytes)
2. rs2_1DvA2.PBS (522 bytes)
3. rs2_1DvA2_rms.err (361 bytes)
4. rs2_1DvA2.1.cntl (2238 bytes)
5. rs2_1DvA2.2.cntl (2238 bytes)

Amber Archive May 2016 by messages with attachments