VMD-L Mailing List

From: soumadwip ghosh (soumadwipghosh_at_gmail.com)
Date: Thu Mar 25 2021 - 02:57:21 CDT

Hi all

Sorry if this email is repetitive. I don't see the email I posted onto the
VMD mailing list a day or so ago.
I have created coordinate and psf files for my system
(step5_input.pdb/psf/crd). However, I would like to add one triple bond
between atom# 22424 and 23768 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,
improper and dihedral info? Is topotool suitable for this purpose? I have
limited experience with these tools (esp toptool or 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 topotool/psfgen script with my system for the triple
covalent bond that I am looking for that would be of tremendous help. I am
not sure what my PATCH statement would be for PSFGEN to work. You may find
the associated files in the attached link. The FF parameters are in the
toppar directory.
https://urldefense.com/v3/__https://drive.google.com/drive/folders/1z6efalqxQsHyGrljsD07zZ6wOCtYV5mC__;!!DZ3fjg!qYcDpY_BkPcgfbdFR9CdF0TOQgZPmUC5ATKmyBup4tH6qAkdLBSw21LM666XTAu7ng$

There are two topotool script in the link that I wrote as well but they did
not get the job done. If you think Topotool should perform the job would
you mind commenting on the script(s) attached for me to figure out what
really went wrong?

Thank you !

Soumadwip Ghosh