[AMBER] MCPB.py generated parameters in leap

From: SARAH JEANNE LEFAVE <s.lefave.utah.edu>
Date: Fri, 5 Jul 2019 17:13:18 +0000

Hi all,

I am parameterizing a protein with 3 different metal centers (two heme sites with different charges on the metal and substituents, and a Cu histidine site) I have finished MCPB.py steps 1-4 and am working on generating the parameter and topology files. I ran 3 separate MCPB.py runs for each of the metal sites as they are distinct active sites from one another. This generated 3 different sets of files for running with tleap. I combined these into one protein_tleap.in adding the additional atoms to be defined and loading all the relevant files in. After getting many errors about **no angle parameters and ** not torsion terms, I redefined the redundant metals and nitrogen’s that were added in the addAtomTypes section such that I now have (M1-M3 and Y1-14). I also modified the mol2 and frcmod files to be consistent for these. While this reduced some of the errors regarding angle parameters and torsion terms I still get a significant amount. I suspect it is due to the redundant cc, ce, cd, ha… and CR, CV, HX… etc. If this is in fact the problem is there another way to change this rather than manually renaming the atoms in the ligand? Will renaming them to non-redunant names cause any other error for recognition with gaff or otherwise?

Thank you!
AMBER mailing list
Received on Fri Jul 05 2019 - 10:30:03 PDT
Custom Search