VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Sat Dec 12 2020 - 11:27:04 CST

W dniu 12.12.2020 o 15:01, Onur Alptürk pisze:
>
> To whom this may concern;
>
> My name is Onur Alpturk and I am an assistant professor at Istanbul
> Technical University. I have been utilizing the script written by you
> to obtain PSF files of nucleic acids and I am experiencing a general
> problem. This is why I am writing to you to seek your assistance.
>
> I have been working on the elastic properties of certain nucleic
> acids. In that regard, I have to carry out some simulation, which
> demands the generation of PSF files, at first. Software, in
> conjunction with some servers I accessed, build dsDNA where the
> nucleobases are labeled as DC or DT, instead of conventional
> nomenclature as C or T, for instance. For this reason, I think that
> the script I have been using failed to generate the proper PSF files.
>
This is expected. Residue names in the topology files must have unique
names, but the standard nomenclature does not differentiate C in RNA and
C in DNA. Therefore for deoxy- nucleotides the force field uses names
DC, DA, DG and DT.

To make sure the PSF is correct you should rather examine the structure,
especially the parts which are modified ("patched") like 3' and 5'
termini and whether you have ribose or deoxyribose rings. Residue names
are important at creation of the PSF to properly match parameters with
atoms, but they are irrelevant later for modeling itself.

With regards,

Pawel

> I was wondering how I can overcome this problem. I would appreciate it
> if you could guide me.
>
> With kindest regards,
>
> Onur
>
> Onur Alpturk, Ph.D.
>
> Istanbul Technical University,
>
> Department of Chemistry, Room: B3-118
>
> Maslak, 34469 Istanbul
>
> Phone: +90 (212) 285 3249
>
> Fax: +90 (212) 285 6386
>
> https://onuralpturk8.wixsite.com/biochemistrygroup
>