Amber Archive Sep 2020: by messages with attachments

[AMBER] best way to umbrella-sample a pseudo-dihedral angle Collective Variable Akshay Prabhakant (Wed Sep 02 2020 - 04:18:17 PDT)
1. 09-01__18-36-04.png (268214 bytes)
[AMBER] Fw: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Esposito Carmen (Wed Sep 02 2020 - 06:17:09 PDT)
1. 3R1_pH74_netcharge.mol2 (6018 bytes)
2. 3R1_pH74_netcharge.pdbqt (3625 bytes)
3. CKO_pH74_netcharge.mol2 (8628 bytes)
4. CKO_pH74_netcharge.pdbqt (4688 bytes)
Re: [AMBER] Questions on deriving charges for aromatic compounds using The RESP Method Lucas Bandeira (Wed Sep 02 2020 - 11:47:45 PDT)
1. benzene.mol2 (1519 bytes)
2. toluene.mol2 (1837 bytes)
Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane (Thu Sep 03 2020 - 08:21:03 PDT)
1. HAR.mol2 (3014 bytes)
Re: [AMBER] Generating topology using tleap Lucas Bandeira (Fri Sep 04 2020 - 10:47:41 PDT)
1. hexane_gaff.prmtop (14760 bytes)
2. hexane_lipid14_gaff.prmtop (14760 bytes)
3. hexane_lipid14.prmtop (14760 bytes)
4. tleap_hexane_lipid14.in (187 bytes)
5. tleap_hexane_gaff_lipid14.in (213 bytes)
6. tleap_hexane_gaff.in (175 bytes)
[AMBER] Simulation of 10 ns DNA - ligand intercalation Erdem Yeler (Mon Sep 07 2020 - 02:42:23 PDT)
1. image.png (233749 bytes)
2. Untitled.png (196982 bytes)
Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane (Mon Sep 07 2020 - 04:20:19 PDT)
1. leap.log (17166 bytes)
Re: [AMBER] Parametrization of GTP and terminal phosphate of DNA David A Case (Mon Sep 07 2020 - 05:31:56 PDT)
1. GTP.frcmod (1728 bytes)
2. GTP.mol2 (4295 bytes)
Re: [AMBER] Parametrization of GTP and terminal phosphate of DNA Jenny 148 (Mon Sep 07 2020 - 09:18:03 PDT)
1. RNA.pdb (204514 bytes)
[AMBER] Strange RMSD tower appearing in simulation Jorge da Rocha (Tue Sep 08 2020 - 08:42:51 PDT)
1. md_290ns_strange_spike.png (47987 bytes)
Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane (Wed Sep 09 2020 - 05:22:21 PDT)
1. final.pdb (3250 bytes)
Re: [AMBER] error tleap MYRIAN TORRES RICO (Fri Sep 11 2020 - 03:46:31 PDT)
1. mdk2_rig.pdb (74444 bytes)
2. mdk4rig.pdb (73327 bytes)
Re: [AMBER] SHAKEH hydrogen clusters pietroa.bii.a-star.edu.sg (Fri Sep 11 2020 - 22:30:55 PDT)
1. Solv_0_100.inpcrd (77036 bytes)
2. Solv_0_100.prmtop (349429 bytes)
[AMBER] preparing parameter files for a ligand Siavoush Dastmalchi (Tue Sep 15 2020 - 09:34:27 PDT)
1. lig.pdb (3877 bytes)
[AMBER] BR atom moved out Nisha Amarnath Jonniya (Thu Sep 17 2020 - 03:46:19 PDT)
1. crystal-4q2a.png (65251 bytes)
Re: [AMBER] constant pH error Kolattukudy P. Santo (Thu Sep 17 2020 - 10:34:55 PDT)
1. jbl2.cpin (16179 bytes)
[AMBER] ddikick.x error during Fe3+ ion parameter derivation using Gamess gagandeep singh (Fri Sep 18 2020 - 06:47:15 PDT)
1. FE_small_opt.log (40042 bytes)
[AMBER] RMSF plot error Fatemeh Arabi (Sun Sep 20 2020 - 02:20:17 PDT)
1. RMSDplot.png (9930 bytes)
2. RMSFplot.png (10038 bytes)
3. RMSFplot2.png (7235 bytes)
Re: [AMBER] antechamber problem with negatively charged nitrogen David A Case (Sun Sep 20 2020 - 07:39:05 PDT)
1. 11.mol2 (1685 bytes)
Re: [AMBER] MMPBSA binding energy was positive for charged ligand Nada Afiva (Mon Sep 21 2020 - 05:45:28 PDT)
1. atp-charge0.dat (10882 bytes)
2. ATP-charge-4.dat (10882 bytes)
[AMBER] tutorials restructured and ConstpH/redox tutorial pages not accessible Vaibhav Dixit (Tue Sep 22 2020 - 23:49:04 PDT)
1. image.png (99771 bytes)
[AMBER] Coordinate resetting cannot be accomplished -reg R A Jeyaram 16PHD0482 (Wed Sep 23 2020 - 03:38:09 PDT)
1. density.in (247 bytes)
2. den.out (48096 bytes)
[AMBER] Heme parameters Siavoush Dastmalchi (Wed Sep 23 2020 - 08:00:19 PDT)
1. sqm.out (750 bytes)
2. t5.pdb (6024 bytes)
3. t5.mol2 (7469 bytes)
[AMBER] xleap aishen (Wed Sep 23 2020 - 13:19:02 PDT)
1. xleap.png (10357 bytes)
Re: [AMBER] xleap Gustaf Olsson (Thu Sep 24 2020 - 00:04:55 PDT)
1. Screenshot1.png (954 bytes)
2. Screenshot2.png (1104 bytes)
Re: [AMBER] xleap aishen (Thu Sep 24 2020 - 01:06:56 PDT)
1. xleapm.png (13841 bytes)
2. xleap (33 bytes)
[AMBER] PMF calculation somdev pahari (Tue Sep 29 2020 - 01:25:15 PDT)
1. PMF.png (54154 bytes)
Re: [AMBER] xleap Gustaf Olsson (Tue Sep 29 2020 - 01:17:51 PDT)
1. leap.png (8452 bytes)

Amber Archive Sep 2020 by messages with attachments