Psfgen, Disulfide Linkages, and the Drude Polarizable Force Field

From: Michael Robinson (
Date: Fri Jun 05 2020 - 03:31:05 CDT

Hi everyone,

Hopefully this one isn't a trivial question - I've contacted normal help
methods, with no solution apparent. I've been testing the use of Drude FF
on insulin crystal structures, using CHARMM-GUI to generate the input
structures. Through some experimentation, I've found out that I cannot
generate solvated insulin crystal structures using CHARMM-GUI if disulfide
linkages are present. This issue occurs in the three crystal structures
I've tried it with (1g7b, 3i3z, and 1mso PDB IDs), and experimenting with
various factors has not been met with success. These disulfide linkages are
integral to the structure, and so I'm searching for a way to combine the
solvated structure with disulfide linkages and the Drude FF. As far as I'm
aware, psfgen is not currently able to handle Drude particles, so I think I
may be out of luck here. I'm not currently easily able to access charmm,
but it would be possible if it is the only solution. Does anyone have any
ideas for namd-compatible methods to either solvate the correctly-linked
protein structure, or apply a (drude-compatible) DISU patch to the solvated

Thank you for your time reading this email, and any help you may be able to
Michael Robinson

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:09 CST