Amber Archive Mar 2017: by messages with attachments

[AMBER] prepare prepin file from MCPB results Abhilash J (Mon Mar 06 2017 - 00:34:14 PST)
1. comp_tleap.in (702 bytes)
2. FE1.mol2 (263 bytes)
3. HM1.mol2 (7366 bytes)
4. comp_mcpbpy.pdb (5058 bytes)
5. HEM.frcmod (1662 bytes)
[AMBER] Error in Cobalt parameters in CO-METHYLCOBALAMIN with MCPB.py Abhilash J (Wed Mar 08 2017 - 01:45:50 PST)
1. CO.mol2 (277 bytes)
2. COB.frcmod (1731 bytes)
3. COB.mol2 (18185 bytes)
4. comp.in (161 bytes)
5. comp_H_renum.pdb (14985 bytes)
6. CO.pdb (67 bytes)
7. COB_2.pdb (12141 bytes)
Re: [AMBER] AmberTools compilation Tom Dreyfus (Thu Mar 09 2017 - 06:41:44 PST)
1. config.txt (2864 bytes)
2. compile.txt (149055 bytes)
3. config.h (6067 bytes)
Re: [AMBER] AmberTools compilation Tom Dreyfus (Thu Mar 09 2017 - 07:22:47 PST)
1. gcc.txt (3645 bytes)
[AMBER] Potential on QM atoms - details about cutoff Elisa Pieri (Fri Mar 10 2017 - 07:13:19 PST)
1. files.tgz (256851 bytes)
[AMBER] Memory footprint goes on increasing: pytraj traj.iterchunk used, distances between bonds calculation SHAILESH KUMAR (Sun Mar 12 2017 - 13:17:30 PDT)
1. profile.log (6999 bytes)
2. code.py (5451 bytes)
3. INR.DFS.tree (3569 bytes)
4. INR.lig.gas.leap.prmtop (23294 bytes)
5. INR.pdb (2680 bytes)
[AMBER] About PCA with cpptraj Elvis Martis (Wed Mar 15 2017 - 09:34:00 PDT)
1. pca.in (2948 bytes)
2. cpptraj.log (4654 bytes)
[AMBER] distance calculations - Protein-RNA Sidhu, Khushwant (Dr.) (Thu Mar 16 2017 - 03:36:26 PDT)
1. image001.gif (3342 bytes)
Re: [AMBER] Problems in using Parmchk2 杨满意 (Thu Mar 16 2017 - 07:13:06 PDT)
1. SeON1.mol2 (1578 bytes)
Re: [AMBER] How to generate inputfile 杨满意 (Fri Mar 17 2017 - 05:34:59 PDT)
1. SeON.frcmod (649 bytes)
2. SeON.mol2 (1578 bytes)
3. SeON.pdb (753 bytes)
4. SeON2.inpcrd (486 bytes)
5. SeON2.prmtop (12420 bytes)
6. tleap.in (132 bytes)
Re: [AMBER] How to generate inputfile (???) 杨满意 (Fri Mar 17 2017 - 06:09:32 PDT)
1. aa.png (9228 bytes)
[AMBER] 2D rms plot doubt Mary Varughese (Sat Mar 18 2017 - 02:56:00 PDT)
1. d.png (285710 bytes)
[AMBER] Issue regarding ligand parameterization Nirupma Singh (Sun Mar 19 2017 - 22:55:18 PDT)
1. ligand__2_.pdb (2113 bytes)
Re: [AMBER] Issue regarding ligand parameterization Bruno Falcone (Mon Mar 20 2017 - 07:21:22 PDT)
1. lig_h.pdb (7786 bytes)
2. lig_p.pdb (2180 bytes)
Re: [AMBER] Problems in using Parmchk2 David Case (Tue Mar 21 2017 - 07:15:51 PDT)
1. SeON1.frcmod (1232 bytes)
[AMBER] multinode pmemd.cuda.MPI jac9999 behavior Scott Brozell (Tue Mar 21 2017 - 12:52:34 PDT)
1. jac9999multinodecudampi.ruby.pbs.test (1735 bytes)
2. jac9999multinodecudampi.ruby.o764074 (22259 bytes)
3. jac9999multinodecudampi.ruby.o765032 (23504 bytes)
[AMBER] DU issue with Antechamber Abhilash J (Wed Mar 22 2017 - 21:21:37 PDT)
1. L3L.prepin (3248 bytes)
Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Scott Brozell (Thu Mar 23 2017 - 15:58:52 PDT)
1. r0214GPU_0.log (1711 bytes)
2. r0218GPU_0.log (1711 bytes)
3. r0214GPU.large_0.log (1711 bytes)
4. r0218GPU.large_0.log (1711 bytes)
Re: [AMBER] How to perform Newton-Raphson minimization to protein 巩梦雪 (Fri Mar 24 2017 - 06:53:26 PDT)
1. 3jvs_wat_box.prmtop (243347 bytes)
2. 3jvs_wat_box.pdb (35513 bytes)
3. test.nab (624 bytes)
4. test.c (1445 bytes)
5. test.out (113813 bytes)
6. out.traj (4 bytes)
Re: [AMBER] DU issue with Antechamber Abhilash J (Sat Mar 25 2017 - 00:16:26 PDT)
1. L3L.pdb (2456 bytes)
[AMBER] Force/energy vs extension curve in steered MD Ramin Salimi (Sat Mar 25 2017 - 10:02:22 PDT)
1. dist.smd3.dat (45600 bytes)
[AMBER] Force/Energy vs extension curve from Steered MD Ramin Salimi (Sat Mar 25 2017 - 10:36:15 PDT)
1. dist.smd3.dat (45600 bytes)
[AMBER] FEW- issues generating parameter files for MD Sowmya Indrakumar (Mon Mar 27 2017 - 06:57:49 PDT)
1. setup_am1_3trj_MDs (3565 bytes)
2. leap_1.log (2552 bytes)
Re: [AMBER] FEW- issues generating parameter files for MD Sowmya Indrakumar (Mon Mar 27 2017 - 08:18:40 PDT)
1. ZINC01482113.mol2 (2214 bytes)
2. ZINC01482113_lig.pdb (1501 bytes)
3. leap_1.log (2552 bytes)
4. leap_1.log (2375 bytes)
[AMBER] RDF plot Sowmya Indrakumar (Tue Mar 28 2017 - 03:35:39 PDT)
1. rdf.png (6772 bytes)
2. protein (5188 bytes)
Re: [AMBER] RDF plot Sowmya Indrakumar (Tue Mar 28 2017 - 05:49:36 PDT)
1. residue_2.png (42911 bytes)
Re: [AMBER] FEW- issues generating parameter files for MD Sowmya Indrakumar (Tue Mar 28 2017 - 08:59:19 PDT)
1. setup_am1_3trj_MDs (3565 bytes)
2. leap_script_1.in (1587 bytes)

Amber Archive Mar 2017 by messages with attachments