Amber Archive Mar 2016 by messages with attachments

Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Mon Feb 29 2016 - 21:37:14 PST)
1. ff14SB.zip (166076 bytes)
2. ff99bsc0.zip (169709 bytes)
[AMBER] I have a problem when installing GPU version of Pmemd(Amber14). yhzahsc (Tue Mar 01 2016 - 00:44:07 PST)
1. IMG_3658.JPG (203244 bytes)
[AMBER] Error while creating neutralized topology and coordinates file Sreemol G (Tue Mar 01 2016 - 03:33:44 PST)
1. 02-25_17-04-28.png (55867 bytes)
[AMBER] MMPBSA error Hira Jabeen (Tue Mar 01 2016 - 21:56:42 PST)
1. mmpbsa.in (168 bytes)
2. pbsa.jp2 (215867 bytes)
Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Wed Mar 02 2016 - 01:48:07 PST)
1. New.log (30906 bytes)
2. old.log (646346 bytes)
[AMBER] Dihedral angle values from .mdcrd file Vasantha Kumar (Wed Mar 02 2016 - 03:47:21 PST)
1. dihedral1.png (16928 bytes)
[AMBER] mmgbsa_error chemjxn (Thu Mar 03 2016 - 00:09:42 PST)
1. mmgbsa_error.jpg (205219 bytes)
2. gbsa.sh (394 bytes)
3. mmpbsa.in (147 bytes)
[AMBER] mmgbsa_error chemjxn (Thu Mar 03 2016 - 00:10:35 PST)
1. mmgbsa_error.jpg (205219 bytes)
2. gbsa.sh (394 bytes)
3. mmpbsa.in (147 bytes)
Re: [AMBER] problem running MD for diphosphoric acid anion necmettin pirinccioglu (Thu Mar 03 2016 - 00:49:28 PST)
1. mdcrd.tar.gz (344707 bytes)
[AMBER] Error while creating topology file after adding ions Sreemol G (Thu Mar 03 2016 - 20:40:03 PST)
1. 02-25_17-04-28.png (55867 bytes)
Re: [AMBER] mmgbsa_error chemjxn (Fri Mar 04 2016 - 01:00:03 PST)
1. mmpbsa.out (453 bytes)
2. _MMPBSA_complex_gb.mdout.0 (1294 bytes)
[AMBER] regarding mm-pbsa calculation neha chaudhary (Fri Mar 04 2016 - 20:58:10 PST)
1. binding_energy.log (1818 bytes)
[AMBER] Production phase for MMPBSA Arati Paudyal (Tue Mar 08 2016 - 11:06:10 PST)
1. image.png (43040 bytes)
[AMBER] Optimize in Gaussian with RESP Jesmita Dhar (Wed Mar 09 2016 - 00:36:50 PST)
1. Go_opt_gaussian.pdb (11640 bytes)
[AMBER] Installation error amber14 Dr. M. K. Yadav (Thu Mar 10 2016 - 00:28:20 PST)
1. 03-09_15-29-53.log (219366 bytes)
2. at_summary (196 bytes)
Re: [AMBER] Optimize in Gaussian with RESP Jesmita Dhar (Thu Mar 10 2016 - 22:47:21 PST)
1. leaprc.q4mdfft (2011 bytes)
2. frcmod.correspondence (1795 bytes)
3. frcmod.known (11569 bytes)
4. frcmod.unknown (1702 bytes)
5. sm_m1-c1.mol2 (7299 bytes)
[AMBER] Fwd: Optimize in Gaussian with RESP Jesmita Dhar (Fri Mar 11 2016 - 00:33:38 PST)
1. leaprc.q4mdfft (2011 bytes)
2. frcmod.correspondence (1795 bytes)
3. frcmod.known (11569 bytes)
4. frcmod.unknown (1702 bytes)
5. sm_m1-c1.mol2 (7299 bytes)
[AMBER] RMSD too high after simulation Arati Paudyal (Fri Mar 11 2016 - 17:41:36 PST)
1. image.png (26379 bytes)
2. image.png (42920 bytes)
[AMBER] TIP3P Wu Xu (Sat Mar 12 2016 - 14:11:44 PST)
1. TIP3P_Problem.pdf (145392 bytes)
Re: [AMBER] Problems when trying to improve angle parameters whith paramfit Robin Betz (Mon Mar 14 2016 - 15:38:56 PDT)
1. file_io.c (13477 bytes)
[AMBER] topology file for a graphene oxide with repetitive pattern Jesmita Dhar (Wed Mar 16 2016 - 03:07:29 PDT)
1. sm_m1-c1.mol2 (7431 bytes)
2. large-vegazz.pdb (12685 bytes)
Re: [AMBER] rmsd y axis value deviation. Saman Yousuf ali (Wed Mar 16 2016 - 03:29:58 PDT)
1. snapshot7.png (17378 bytes)
[AMBER] nitro tyrosine Wu Xu (Thu Mar 17 2016 - 19:06:00 PDT)
1. resp.out (602998 bytes)
2. nty.frcmod (4860 bytes)
3. nty.inpcrd (788 bytes)
4. nty.prepin (2258 bytes)
5. nty.prmtop (17774 bytes)
6. nty.jpg (38175 bytes)
[AMBER] restart file error Sidhu, Khushwant (Dr.) (Fri Mar 18 2016 - 03:59:37 PDT)
1. image002.gif (3340 bytes)
Re: [AMBER] MMPBSA doubt Mary Varughese (Fri Mar 18 2016 - 21:48:15 PDT)
1. mm_pbsa1.in (11479 bytes)
2. mm_pbsa2.in (5315 bytes)
[AMBER] FW: problem in plotting total energy graph by using perl script Sehrish Naz Aijaz (Sat Mar 19 2016 - 01:20:41 PDT)
1. summary.png (10619 bytes)
[AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Sat Mar 19 2016 - 01:25:27 PDT)
1. summary__162883_.png (10619 bytes)
2. 994690DB57A74C5ABD3E5D9B494D891B.png (40338 bytes)
Re: [AMBER] On alphabetizing impropers David Cerutti (Thu Mar 24 2016 - 07:47:20 PDT)
1. YOPRO.pdb (4700 bytes)
2. YOPRO_60_0_resultbox.prmtop (33512 bytes)
[AMBER] Amber MD simulation - viewing artifacts in VMD? Enrique Frio (Tue Mar 29 2016 - 05:05:05 PDT)
1. 9-2.png (112120 bytes)
Re: [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Wed Mar 30 2016 - 00:49:34 PDT)
1. energy_tot.png (8329 bytes)
2. energy_incomplete.png (9036 bytes)
Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Wed Mar 30 2016 - 20:13:23 PDT)
1. parmed.jpg (120489 bytes)
2. mol21.frcmod (18459 bytes)

Last message date: Thu Mar 31 2016 - 22:00:05 PDT
Archived on: Sun Nov 24 2024 - 05:55:32 PST

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