CHARMM36 to Drude conversion for NAMD

From: Almeida-HernŠndez, Yasser, Dr. (yasser.almeida-hernandez_at_uni-due.de)
Date: Tue Oct 06 2020 - 03:37:32 CDT

Hi all,

I have a solvated and neutralized system that I used with CHARMM36 FF in NAMD. Now I want to use the same system but using Drude FF. Is there any easy tool/script to convert from CHARMM36 to Drude?

According to psfgen User's Guide version 2.0:

"Atom modification operations, e.g., psfset, and queries with the segment command on the drude particles, are not implemented. We advise the user to use VMD to assign beta and occupancy values during the structure preparation. writemol and readmol commands are not compatible with structure preparation for Drude Force field."

Thanks a lot in advance.

Bests.

--
Dr. Yasser Almeida-Hernandez
Postdoctoral Researcher
Computational Biochemistry group
T01 R03 D45
Faculty of Biology
University of Duisburg-Essen
Universitštsstr. 2, 45117 Essen
Email: yasser.almeida-hernandez_at_uni-due.de<mailto:%20yasser.almeida-hernandez_at_uni-due.de>
Phone: +49 201 183 2457<tel:+49%20201%20183%202457>

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:10 CST