Amber Archive Jun 2021: by messages with attachments

Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Akinyemi Omoniyi (Sat Jun 05 2021 - 15:15:00 PDT)
1. min2.out (16043 bytes)
[AMBER] How to fix the numbering of amino acid that got shifted in topology file that created in amber Tleap priya murugan (Sun Jun 06 2021 - 21:11:34 PDT)
1. 69m_ori_file_x_hydrogen_.png (47517 bytes)
2. 69M_topology.png (38575 bytes)
3. heme_topology_file.png (44667 bytes)
4. heme_ori_x_h.png (54368 bytes)
[AMBER] What does the UVV file output for a LJ only system and why cant I recreate it? Daniel Fowles (Mon Jun 07 2021 - 04:59:26 PDT)
1. 677E3D2D19CB40DFA823CAD6A3101A29.png (2070 bytes)
2. DD03843984994C1C80A1E97B861ACB01.png (2350 bytes)
3. DB9019300A074F32B8EF9270DB7D9ACC.png (3073 bytes)
Re: [AMBER] [MCPB.py]_KeyError: 'HZ3' sabrine kh (Mon Jun 07 2021 - 08:40:48 PDT)
1. 6ye2_fixed_H.pdb (664326 bytes)
[AMBER] Error in calculating pair distribution function Umesh Roy (Mon Jun 07 2021 - 21:11:42 PDT)
1. pairdist.png (6874 bytes)
Re: [AMBER] [MCPB.py]_KeyError: 'HZ3' sabrine kh (Tue Jun 08 2021 - 06:16:42 PDT)
1. 6ye2_WAT.mol2 (470 bytes)
2. 6ye2_ligand.mol2 (3428 bytes)
3. 6ye2_ligand.frcmod (1293 bytes)
4. 6ye2.in (187 bytes)
5. 6ye2_ZN.mol2 (348 bytes)
[AMBER] Error in pdb4amber for AmberTools21 Bhattacharjee, Sinjini (Wed Jun 09 2021 - 06:26:09 PDT)
1. fixed.pdb (118460 bytes)
Re: [AMBER] Error: Could not open file frcmod.ions1lm_126_hfe_opc: not found Pengfei Li (Wed Jun 09 2021 - 15:52:32 PDT)
1. leaprc.water.opc (1948 bytes)
2. leaprc.water.fb3 (1942 bytes)
3. leaprc.water.fb4 (1970 bytes)
[AMBER] The code for modeling circular DNA is in the attachment 韩正威 (Thu Jun 10 2021 - 00:19:35 PDT)
1. DNA.nab (1457 bytes)
Re: [AMBER] NAB superimpose issue Mandar Kulkarni (Thu Jun 10 2021 - 02:07:38 PDT)
1. align.png (76316 bytes)
2. alignframe.nab (633 bytes)
[AMBER] Restart the crashed MD run in Amber18 Amir Zeb (Mon Jun 14 2021 - 23:42:47 PDT)
1. image.png (10795 bytes)
[AMBER] Fluctuation in GPU usage Aravind R (Tue Jun 15 2021 - 10:34:45 PDT)
1. Amber___gromacs.png (68941 bytes)
2. Input_script.png (135181 bytes)
3. Speed.png (77717 bytes)
4. Only_amber.png (62030 bytes)
5. Top_results.png (94115 bytes)
Re: [AMBER] Restart the crashed MD run in Amber18 Amir Zeb (Thu Jun 17 2021 - 18:04:39 PDT)
1. image.png (91221 bytes)
[AMBER] RMSD plot in ns Sadaf Rani (Sun Jun 20 2021 - 04:58:20 PDT)
1. image.png (43330 bytes)
Re: [AMBER] Preparation of i-Motif structures Sruthi Sudhakar (Tue Jun 22 2021 - 11:37:02 PDT)
1. im2.pdb (53625 bytes)
[AMBER] ambertools20 - request for older version Ruben Cruz (Wed Jun 23 2021 - 04:57:52 PDT)
1. cmake.log (2765 bytes)
2. CMakeError.log (36574 bytes)
3. CMakeOutput.log (26200 bytes)
Re: [AMBER] Installation error AMBERTOOLS21 Mandar Kulkarni (Thu Jun 24 2021 - 11:38:46 PDT)
1. install.log.gz (712396 bytes)
[AMBER] Multi-Monomer Polymer Swisher, Justin S (Thu Jun 24 2021 - 12:54:04 PDT)
1. hvcl_retry.prepi (2366 bytes)
2. vace.prepi (1604 bytes)
3. solu20_tleap.out (2704 bytes)
Re: [AMBER] sqm seeks the Boron parameter file instead of Bromine Thomas Evangelidis (Mon Jun 28 2021 - 05:29:41 PDT)
1. input.pdb.gz (114638 bytes)
[AMBER] Installing compilers/libraries on Ubuntu 18.04 without root access Smith, Ally (Mon Jun 28 2021 - 11:52:52 PDT)
1. config.site.txt (125 bytes)

Amber Archive Jun 2021 by messages with attachments