From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Sat Dec 12 2020 - 12:34:37 CST

W dniu 12.12.2020 o 18:35, Onur Alptürk pisze:
>
> Dear Pawel;
>
> Thank you very much for your input; that helped a lot.
>
> Frankly speaking, I didn’t experience this problem with 3D-DART, which
> is out of service at the moment. Many others, such as Avogrado and
> Discovery Studio, caused this problem. In that case, can you just me a
> software/server to build DNA in proper way? Would Amber do the work?
>
How you create the structure is only relevant to what you will do with
it later. You mentioned making PSF file; this format is used by charmm
and namd, but not by Amber. So if you want to do your modeling with namd
or charmm, the PSF file may work as is - unless you try to use it with a
different force field that it was created for. If you want do the
modeling in Discovery Studio, generate your structure there and it will
work. Amber would do the work for modeling with Amber but using a
different file format and force field. I'm not familiar with Amber but I
do remember some residue names are different in Amber force field than
in the CHARMM force field. Again, its just forcefield-specific naming
even if for chemically identical structure.

Otherwise, if you mix different tools then problems may indeed arise,
but you didn't specify any details so no one will be able to guide you.

With regards,

Pawel

> Many thanks,
>
> 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
>
> *From:* pawel.kedzierski_at_pwr.edu.pl <pawel.kedzierski_at_pwr.edu.pl>
> *Sent:* Saturday, December 12, 2020 8:27 PM
> *To:* Onur Alptürk <onur.alpturk_at_itu.edu.tr>
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: FW: Seeking assistance
>
> 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
>