Amber Archive Jul 2016 by messages with attachments

[AMBER] cpptraj.hbond: water in the complex chemjxn (Thu Jun 30 2016 - 18:10:42 PDT)
1. cpptraj.hbond1.in (995 bytes)
2. 1ksn_o_complex.pdb (187931 bytes)
[AMBER] Help: make test fails during parallel amber installation Dr. M. K. Yadav (Thu Jun 30 2016 - 20:52:03 PDT)
1. 06-30_22-54-49.log (98394 bytes)
2. 06-30_22-54-21.log (251117 bytes)
Re: [AMBER] can MCPB build non amino-acid containing complex? Zhenyu Meng (Sat Jul 02 2016 - 06:49:56 PDT)
1. pt1p1_H.pdb (4946 bytes)
2. RES.mol2 (6085 bytes)
3. PT.mol2 (276 bytes)
[AMBER] Question about Charge derivation for GLYCAM force field Casalini Tommaso (Mon Jul 04 2016 - 07:03:00 PDT)
1. HAL.mol2 (2601 bytes)
Re: [AMBER] MCPB Marcelo Andrade Chagas (Mon Jul 04 2016 - 13:02:54 PDT)
1. image.png (40703 bytes)
2. image.png (32601 bytes)
3. image.png (9149 bytes)
Re: [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py Bilal Nizami (Wed Jul 06 2016 - 05:37:19 PDT)
1. 1caq.pdb (169371 bytes)
2. 2oeo.pdb (125064 bytes)
3. pdb426d.ent (68202 bytes)
4. 966c.pdb (202257 bytes)
[AMBER] Stuck somewhere using antechamber Xiaoyu Wang (Wed Jul 06 2016 - 16:00:37 PDT)
1. jp0637173_si_001.pdb (81816 bytes)
Re: [AMBER] Amber16 tutorials Corum, Katharine W (Thu Jul 07 2016 - 08:13:15 PDT)
1. NMA_skeleton.pdb (114 bytes)
[AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice (Thu Jul 07 2016 - 10:49:07 PDT)
1. diffusion_files.zip (393063 bytes)
[AMBER] rmsd plot error Saman Yousuf ali (Fri Jul 08 2016 - 03:55:51 PDT)
1. rmsd.png (24334 bytes)
Re: [AMBER] rmsd plot error Saman Yousuf ali (Fri Jul 08 2016 - 04:42:08 PDT)
1. rmsd.png (24334 bytes)
Re: [AMBER] rmsd plot error Saman Yousuf ali (Fri Jul 08 2016 - 05:58:19 PDT)
1. strip.png (22721 bytes)
[AMBER] ligand bond distortion during MD run. Saman Yousuf ali (Fri Jul 08 2016 - 10:48:21 PDT)
1. dist.png (22773 bytes)
Re: [AMBER] Library errors while using NAB on Amber16 David A Case (Fri Jul 08 2016 - 13:22:49 PDT)
1. setbounds.patch (707 bytes)
Re: [AMBER] addAtomType problem Lea Natalia Toledo Carvajal (Fri Jul 08 2016 - 15:18:25 PDT)
1. mix.txt (2538 bytes)
2. input (569 bytes)
3. leap.txt (45987 bytes)
[AMBER] adding non-standard residue to RNA strand Martina Devi (Sat Jul 09 2016 - 10:21:28 PDT)
1. OAU.mol2 (3935 bytes)
[AMBER] RMSD plot query esther nehu (Thu Jul 14 2016 - 07:29:41 PDT)
1. rms_copy.jpg (620734 bytes)
Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice (Thu Jul 14 2016 - 09:13:57 PDT)
1. LPS_bottom.pdf (69760 bytes)
2. LPS_top.pdf (66412 bytes)
[AMBER] Regarding Parameter file not saved Vishal Nemaysh (Sun Jul 17 2016 - 10:52:32 PDT)
1. lignew.pdb (229835 bytes)
Re: [AMBER] Regarding Parameter file not saved Vishal Nemaysh (Mon Jul 18 2016 - 03:09:37 PDT)
1. lignew.pdb (230669 bytes)
2. lig.frcmod (10018 bytes)
3. lig.mol2 (3412 bytes)
Re: [AMBER] Regarding Parameter file not saved Vishal Nemaysh (Mon Jul 18 2016 - 08:17:02 PDT)
1. lignew.pdb (230600 bytes)
2. lig.frcmod (1225 bytes)
3. lig.mol2 (3412 bytes)
[AMBER] MCPB.py - coordinate sphere FE Anna Cebrian Prats (Wed Jul 20 2016 - 05:44:01 PDT)
1. MCPB.tar.gz (226690 bytes)
Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice (Wed Jul 20 2016 - 11:34:14 PDT)
1. LPS_bottom_nocenter.pdf (58409 bytes)
2. LPS_comparison.pdf (168012 bytes)
3. LPS_top_nocenter.pdf (59465 bytes)
4. mLPS_bottom_nocenter.pdf (55462 bytes)
5. mLPS_comparison.pdf (165086 bytes)
6. mLPS_top_nocenter.pdf (58453 bytes)
Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice (Wed Jul 20 2016 - 11:57:32 PDT)
1. stfcdiffusion_LPS.pdf (116655 bytes)
Re: [AMBER] MDCRD nida baig (Sat Jul 23 2016 - 00:46:45 PDT)
1. protein.jpeg (506796 bytes)
[AMBER] ntr vs ibelly. Saman Yousuf ali (Tue Jul 26 2016 - 03:45:06 PDT)
1. 1.png (308952 bytes)
Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith (Tue Jul 26 2016 - 11:11:37 PDT)
1. gcg.dip.o.save (40680 bytes)
2. gcg.dip.o (41307 bytes)
3. gcg.dip.o.noREST (36865 bytes)
Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar (Fri Jul 29 2016 - 14:25:26 PDT)
1. cpptraj.log (10519 bytes)
2. rmsd_all.in (602 bytes)
Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar (Fri Jul 29 2016 - 14:33:19 PDT)
1. rmsd.dat (24461 bytes)

Last message date: Sun Jul 31 2016 - 07:00:03 PDT
Archived on: Sun Nov 24 2024 - 05:55:36 PST

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