Amber Archive Sep 2019: by messages with attachments

[AMBER] running NAMD with AMBER inputs Rui Chen (Sun Sep 01 2019 - 10:29:28 PDT)
1. min.conf (3387 bytes)
[AMBER] Generating parameters for iron-sulfur protein 崔佳文 (Mon Sep 02 2019 - 21:11:10 PDT)
1. 1a70.pdb (92826 bytes)
[AMBER] Problem with CPPTRAJ (RMSD) Rui Chen (Mon Sep 02 2019 - 22:21:47 PDT)
1. 09-02_at_11.10.28_PM.png (24044 bytes)
2. 09-02_at_11.11.11_PM.png (11567 bytes)
[AMBER] Ligand parameterization Hira Jabeen (Tue Sep 03 2019 - 03:56:42 PDT)
1. leap.log (17409 bytes)
2. MEM.frcmod (2731 bytes)
3. MEM.mol2 (5726 bytes)
Re: [AMBER] how to load amber rst file in vmd for observing box size Sadaf Rani (Fri Sep 06 2019 - 12:55:30 PDT)
1. Energy_EPOT.png (114321 bytes)
Re: [AMBER] How to generate parameter files of modified terminal amino acid residue using Antechamber Shankha Banerjee (Fri Sep 06 2019 - 23:00:26 PDT)
1. 5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.pdb (5613 bytes)
2. 5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.mc (280 bytes)
3. 5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.ac (6171 bytes)
[AMBER] Query regarding plot Airy Sanjeev (Tue Sep 10 2019 - 04:44:19 PDT)
1. pmf_WT.jpg (48854 bytes)
[AMBER] PCA calculation projection Aashish Bhatt (Wed Sep 11 2019 - 03:22:35 PDT)
1. 2D.png (22524 bytes)
2. eigen.png (12082 bytes)
3. first.cpptraj (6848 bytes)
[AMBER] How to generate parameter files of N-terminal modified amino acid residue? Shankha Banerjee (Thu Sep 12 2019 - 00:56:30 PDT)
1. 5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.mc (280 bytes)
2. 5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.ac (6171 bytes)
3. 5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.pdb (5613 bytes)
4. pro-1.pdb (50173 bytes)
5. pro-1_out.pdb (42700 bytes)
Re: [AMBER] Question about unusual RMSD behaviour Amit Kumar (Tue Sep 17 2019 - 02:14:25 PDT)
1. system_compare.png (199990 bytes)
[AMBER] ANTECHAMBER_AC 2018808152.njau.edu.cn (Thu Sep 19 2019 - 05:38:07 PDT)
1. ANTECHAMBER_AC.AC (4748 bytes)
2. EstJ6.pdb (217988 bytes)
3. EstJ6_DBP_bound_sus.pdb (318606 bytes)
4. DBP.pdb (1648 bytes)
[AMBER] EstJ6_DBP_bound_sus 2018808152.njau.edu.cn (Fri Sep 20 2019 - 02:18:46 PDT)
1. EstJ6_DBP_bound_sus.pdb (218009 bytes)
[AMBER] md distorted MYRIAN TORRES RICO (Mon Sep 23 2019 - 03:54:20 PDT)
1. DISTORTED.jpg (56749 bytes)
[AMBER] Unable to generate parameters of modified amino acids using LEAP Shankha Banerjee (Mon Sep 23 2019 - 07:04:07 PDT)
1. leap.log (11825 bytes)
2. leap_g.in (155 bytes)
3. try_out.pdb (40476 bytes)
[AMBER] EstJ6_DBP_bound_sus 2018808152.njau.edu.cn (Tue Sep 24 2019 - 01:34:36 PDT)
1. ANTECHAMBER_AC.AC (4748 bytes)
2. EstJ6.pdb (217988 bytes)
3. DBP.pdb (1648 bytes)
4. EstJ6_DBP_bound_sus.pdb (218009 bytes)
Re: [AMBER] MMGBSA energy calculation problem for RNA Liao (Wed Sep 25 2019 - 19:13:53 PDT)
1. image1.jpeg (153586 bytes)
[AMBER] -Antechamber error for modified residues Patil Pranita Uttamrao (Wed Sep 25 2019 - 23:16:49 PDT)
1. G7M.cif (9537 bytes)
2. frcmod1.g7m (823 bytes)
3. frcmod2.g7m (1028 bytes)
4. frcmod.g7m (12139 bytes)
5. g7m.mol2 (4676 bytes)
6. g7m.ac (4829 bytes)
7. G7M.prepin (3416 bytes)
[AMBER] BORON parameters Monika Choudhary (Thu Sep 26 2019 - 02:41:29 PDT)
1. parmchk.png (48611 bytes)
Re: [AMBER] TI residue mutation with pmemd on GPU Hosein Geraili Daronkola (Thu Sep 26 2019 - 07:33:59 PDT)
1. TI.zip (256120 bytes)
Re: [AMBER] cpptraj rms with different pdb Daniel Roe (Thu Sep 26 2019 - 10:58:30 PDT)
1. ref_and_traj.jpg (28416 bytes)

Amber Archive Sep 2019 by messages with attachments