VMD-L Mailing List

From: soumadwip ghosh (soumadwipghosh_at_gmail.com)
Date: Wed Mar 24 2021 - 04:02:20 CDT

Hi all,

I have created coordinate and psf files for my system
(step5_input.pdb/psf). However, I would like to add one triple bond between
atom# 22442 and 22453 and also obtain the updated PSF and CRD files. I
tried using molfracture and topotools but I am having difficulty perhaps
due to the large size of the system. My question is there a way to get a
CRD and a PSF file for the system with the above new bond, angle and
dihedral info? Is psfgen suitable for this purpose? I have limited
experience with these tools (esp psfgen) and that's why I am asking for
your help. If you can provide me with some help on how to write a sample
psfgen script with my system or in general that would be of tremendous
help. You may find the associated files in the attached link.
 https://urldefense.com/v3/__https://drive.google.com/drive/folders/1DcrScfbGb-ESjSJLHl3UYdyzDwJu08cJ__;!!DZ3fjg!r-J-bnqfqUBSODycYuoKg-xkbcmhGKHqWTTSefdSLBvS3zFCgX_erylZ5-I9EIMa_A$

I will appreciate any kind of help on this.

Thank you
Soumadwip Ghosh