VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 26 2021 - 14:01:39 CDT

a) you are emailing from a gmail account. gmail will never show you your
own emails that you send to mailing lists.

b) what you want to do is a *major* change to your structure and is not
simply done by just rearranging some bonds in the bond topology. this
changes atom types and will require adjustments of the partial charges and
possibly may need reparameterization of the entire functional group you are
changing. this requires in-depth understanding of the force field you use
and the process of force field parameterization. I have no time to debug
your files, let alone figure out where you go wrong, but even if you manage
to update the bond topology correctly (note: .psf files will *not* store
bond order, they just store whether a bond exists, the bond parameters and
hence the bond order is implied by the atom types used) with topotools as
needed, it will result in a bogus .psf file due to the other required and
non-trivial changes.

Axel.

On Thu, Mar 25, 2021 at 4:12 AM soumadwip ghosh <soumadwipghosh_at_gmail.com>
wrote:

> 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!vhd9wFWBI87_ck_kKYB0_BFmk-wOAVd4VypT9IV0aX3qlmYKhkxxsjKXBh_hHdByBw$
> <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
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vhd9wFWBI87_ck_kKYB0_BFmk-wOAVd4VypT9IV0aX3qlmYKhkxxsjKXBh-LtNVCkw$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.