Amber Archive Dec 2020: by messages with attachments

Re: [AMBER] TI electrostatic free energy Franz Waibl (Tue Dec 01 2020 - 04:57:37 PST)
1. electrostatic-ti.png (12120 bytes)
[AMBER] Imaging issue in DNA - cpptraj Satyaseelan C (Tue Dec 01 2020 - 23:17:22 PST)
1. nowaterbox.png (92301 bytes)
2. waterbox.png (133732 bytes)
[AMBER] Missing Iron (Fe) DFTB3 parameters for QM/MM simulation of Enzyme Hafiz Saqib Ali (Thu Dec 03 2020 - 15:04:54 PST)
1. DFTB3.in (643 bytes)
[AMBER] lj1264 in vacuum Brian Radak (Tue Dec 08 2020 - 13:29:25 PST)
1. scan.png (39680 bytes)
[AMBER] Negative values in RDF analyses? Gustaf Olsson (Wed Dec 09 2020 - 05:44:49 PST)
1. rdfs.png (38981 bytes)
[AMBER] B-ob-si-c3 dihedral parametization RESP/Scan problem Erdem Yeler (Thu Dec 10 2020 - 02:22:30 PST)
1. image.png (29309 bytes)
Re: [AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA (Thu Dec 10 2020 - 02:18:17 PST)
1. time_slice_37.png (273943 bytes)
Re: [AMBER] An error during NPT/production (GPU run) Женя Елизарова (Fri Dec 11 2020 - 05:43:29 PST)
1. bondRemap.cpp (155788 bytes)
[AMBER] RMSD Protein-DNA complex Plot Manisha (Mon Dec 14 2020 - 01:16:06 PST)
1. image.png (84211 bytes)
[AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Sun Dec 13 2020 - 22:31:52 PST)
1. _MMPBSA_complex_gb.mdout.0 (5887 bytes)
Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Mon Dec 14 2020 - 01:31:57 PST)
1. mdread2.F90 (118072 bytes)
Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis (Mon Dec 14 2020 - 05:31:40 PST)
1. image.png (70729 bytes)
2. image.png (115374 bytes)
3. mdread2.F90 (118271 bytes)
Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Mon Dec 14 2020 - 19:56:32 PST)
1. image.png (70729 bytes)
2. image.png (115374 bytes)
Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis (Mon Dec 14 2020 - 23:33:19 PST)
1. image.png (70729 bytes)
2. image.png (115374 bytes)
Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Mon Dec 14 2020 - 21:38:04 PST)
1. image.png (70729 bytes)
2. image.png (115374 bytes)
Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Tue Dec 15 2020 - 01:36:25 PST)
1. image.png (70729 bytes)
2. image.png (115374 bytes)
[AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating Chris Lee (Tue Dec 15 2020 - 15:00:32 PST)
1. heat.in (272 bytes)
2. heat.out (10006 bytes)
3. min2.in (81 bytes)
4. min2.out (26412 bytes)
5. runMD.sh (1246 bytes)
[AMBER] Getting error while compile AMBER20 with cuda support Raman Jangra (Tue Dec 15 2020 - 21:16:10 PST)
1. 2D17-4F82-A43E-CED5870C2F8F.jpeg (36254 bytes)
[AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi (Tue Dec 15 2020 - 22:20:02 PST)
1. image.png (64389 bytes)
2. image.png (84211 bytes)
[AMBER] nc files contain lesser number of atoms compared to prmtop Sruthi Sudhakar (Wed Dec 16 2020 - 22:16:53 PST)
1. gamd.in (355 bytes)
Re: [AMBER] positive Amber FF energies? Vaibhav Dixit (Wed Dec 16 2020 - 19:28:46 PST)
1. image.png (98365 bytes)
2. image.png (224769 bytes)
3. image.png (88213 bytes)
[AMBER] strange jump in the rmsd protein complex Vaibhav Dixit (Thu Dec 17 2020 - 23:36:25 PST)
1. image.png (84038 bytes)
2. image.png (307330 bytes)
3. image.png (317049 bytes)
Re: [AMBER] strange jump in the rmsd protein complex Vaibhav Dixit (Fri Dec 18 2020 - 08:47:21 PST)
1. image.png (89206 bytes)
[AMBER] Minimization Time Limit Error with Sander Aanshi Gandhi (Fri Dec 18 2020 - 12:39:57 PST)
1. HC1_minall.in (556 bytes)
2. HC1_minwat.in (960 bytes)
3. submit_min.sh (987 bytes)
Re: [AMBER] Minimization Time Limit Error with Sander Aanshi Gandhi (Fri Dec 18 2020 - 13:19:01 PST)
1. HC1_minwat.out (7824 bytes)
2. HC1_minall.out (7400 bytes)
Re: [AMBER] Electrostatic distance plot Sruthi Sudhakar (Wed Dec 23 2020 - 06:19:34 PST)
1. IMG_3814.jpg (24987 bytes)
[AMBER] Amber20 Installation Error Li,Haoxi (Mon Dec 28 2020 - 17:32:22 PST)
1. cmake.log (96141 bytes)
Re: [AMBER] Amber20 Installation Error David A Case (Wed Dec 30 2020 - 09:21:04 PST)
1. CMakeLists.txt (2645 bytes)
Re: [AMBER] Amber20 Installation Error Li,Haoxi (Wed Dec 30 2020 - 17:49:24 PST)
1. 12-30_19-52-34.log (574412 bytes)
2. 12-30_19-52-34.diff (137675 bytes)
Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi (Thu Dec 31 2020 - 01:53:45 PST)
1. image.png (48214 bytes)
Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi (Thu Dec 31 2020 - 01:54:41 PST)
1. image.png (48214 bytes)

Amber Archive Dec 2020 by messages with attachments