Amber Archive Jul 2019: by messages with attachments

Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Sadaf Rani (Tue Jul 02 2019 - 11:23:31 PDT)
1. 2.dat (1541 bytes)
2. complex_min_all.out (8874 bytes)
Re: [AMBER] REMD error koushik kasavajhala (Tue Jul 02 2019 - 13:23:29 PDT)
1. rem_2rep_gb.tar.gz (13616 bytes)
[AMBER] Error in prmtop and inpcrd atom shivangi agarwal (Wed Jul 03 2019 - 10:06:19 PDT)
1. ZN.in (488 bytes)
2. ligand.prmtop (19345 bytes)
3. ligand.mol2 (3971 bytes)
4. ligand.inpcrd (1508 bytes)
5. ligand.frcmod (673 bytes)
6. ligand2.pdb (6661 bytes)
7. lig.pdb (159333 bytes)
Re: [AMBER] Glycan naming problem Rui Chen (Thu Jul 04 2019 - 09:56:37 PDT)
1. g1dr9.in (422 bytes)
2. leap.log (133348 bytes)
Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Sadaf Rani (Thu Jul 04 2019 - 11:59:20 PDT)
1. complex_min_all.out (8874 bytes)
[AMBER] Fwd: amber installation problem Charu Sharma (JRF) (Sat Jul 06 2019 - 00:26:21 PDT)
1. 07-06_12-52-50.png (151352 bytes)
[AMBER] Fwd: Charu Sharma (JRF) (Sat Jul 06 2019 - 04:20:57 PDT)
1. 07-06_16-48-43.png (93683 bytes)
[AMBER] RESP charges Sadaf Rani (Sun Jul 07 2019 - 11:45:38 PDT)
1. resp.out (6395 bytes)
2. bg6.prepi (2329 bytes)
Re: [AMBER] Error in prmtop and inpcrd atom shivangi agarwal (Mon Jul 08 2019 - 00:34:23 PDT)
1. terminal_commands.txt (10484 bytes)
Re: [AMBER] Error in prmtop and inpcrd atom shivangi agarwal (Tue Jul 09 2019 - 05:45:52 PDT)
1. error.txt (279037 bytes)
2. complex.pdb (309352 bytes)
[AMBER] amber14sb.ff Dylan Tasse (Tue Jul 09 2019 - 07:41:45 PDT)
1. 9.png (168874 bytes)
Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank] Anthony Bogetti (Tue Jul 09 2019 - 08:52:26 PDT)
1. protein.pdb (291064 bytes)
Re: [AMBER] Error in prmtop and inpcrd atom shivangi agarwal (Wed Jul 10 2019 - 00:00:37 PDT)
1. commands (3017 bytes)
2. leap.log (16087 bytes)
3. complex_42_final_2_noH.pdb (157279 bytes)
4. ligand.pdb (3680 bytes)
[AMBER] Error in saving prmtop and inpcrd shivangi agarwal (Fri Jul 12 2019 - 01:42:24 PDT)
1. leap.log (159709 bytes)
Re: [AMBER] Error in saving prmtop and inpcrd shivangi agarwal (Fri Jul 12 2019 - 04:15:03 PDT)
1. leap.log (26851 bytes)
[AMBER] Problem with Phenylphosphonic acid Gustaf Olsson (Fri Jul 12 2019 - 06:15:34 PDT)
1. ppa.frcmod (301 bytes)
2. ppa.pdb (1122 bytes)
3. ppa.prepi (1762 bytes)
[AMBER] How to change the coordinates of the system Maria Bzówka (Mon Jul 15 2019 - 04:32:32 PDT)
1. vmd.png (344935 bytes)
Re: [AMBER] How to change the coordinates of the system Maria Bzówka (Mon Jul 15 2019 - 06:52:56 PDT)
1. vmd2.png (630131 bytes)
Re: [AMBER] memtestG80 alternative ? - testing actual GPUs regarding soft errors Dow Hurst (Mon Jul 15 2019 - 11:32:21 PDT)
1. smi_RTX2080TI-Validation-start.png (35764 bytes)
[AMBER] close contact between atoms Sadaf Rani (Mon Jul 15 2019 - 13:22:05 PDT)
1. leap.log (144859 bytes)
[AMBER] Problem with barostat during the production stage (membrane simulation) Maria Bzówka (Wed Jul 17 2019 - 06:10:52 PDT)
1. step7_production.mdin (2083 bytes)
[AMBER] How to prepare correct gaussian input for RESP charge calculation? Sadaf Rani (Wed Jul 17 2019 - 12:03:34 PDT)
1. floB.txt (113 bytes)
2. floB.mol2 (4396 bytes)
[AMBER] Error: "Bad data for namelist object statene" with constant pH RE simulation Jardin, Christophe Dr. (Fri Jul 19 2019 - 04:30:12 PDT)
1. xxxx.cpin (5129 bytes)
Re: [AMBER] How to change the coordinates of the system Maria Bzówka (Fri Jul 19 2019 - 04:34:55 PDT)
1. vmd3.png (636579 bytes)
[AMBER] Energy different between igb=0 and igb=6 during vacuum minimization with sander Jingxiao Bao (Fri Jul 19 2019 - 06:52:44 PDT)
1. COM_min_sander_igb0_eedmeth4_cut10.out (12253 bytes)
2. COM_min_sander_igb0_eedmeth4_cut9999.out (12249 bytes)
3. COM_min_sander_igb6_cut10.out (11354 bytes)
4. COM_min_sander_igb6_cut9999.out (11232 bytes)
Re: [AMBER] Error in preparing system using AmberTools19 shivangi agarwal (Tue Jul 23 2019 - 20:50:12 PDT)
1. leap.log (113921 bytes)
[AMBER] Kinetic Energy is zero in production run. Amit Kumar (Sat Jul 27 2019 - 04:38:18 PDT)
1. unrestrained_rmsd.png (30368 bytes)
Re: [AMBER] Error in preparing system using AmberTools19 shivangi agarwal (Sun Jul 28 2019 - 21:51:30 PDT)
1. protein-ligand.log (22830 bytes)
2. ligand-ZN.log (20625 bytes)
3. protein.log (22568 bytes)
Re: [AMBER] Error in preparing system using AmberTools19 shivangi agarwal (Sun Jul 28 2019 - 22:34:03 PDT)
1. leap.log (13175 bytes)
[AMBER] Non-standard Hydrogen Bonding Loris Moretti (Tue Jul 30 2019 - 05:25:46 PDT)
1. pyrimidine_charges.png (48197 bytes)

Amber Archive Jul 2019 by messages with attachments