VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Sat Aug 16 2014 - 04:29:29 CDT

Yes, you can/should read multiple topology files.
Look into the following file: stream/toppar_all36_prot_na_combined.str
It lists the files you have to specify first.

On Aug 16, 2014, at 3:48 AM, Ashar Malik <asharjm_at_gmail.com> wrote:

> I am not too comfortable making changes like that.
>
> From the user's guide I can see that the command line approach (psfgen) allows me to provide the topology file through
>
> "topology toppar/top_all22_prot.inp"
>
> I am guessing using the current version for the nucleic acids should work.
>
> However I am still unclear on 1 thing. Can I read in multiple topology files. Since with the C36 update everything has been split up. So a protein bound to a DNA will have to be provided two topologies (one for the protein and one for the DNA) or do I have to generate seperate PSF files for the protein and DNA and then merge them ?
>
> Best,
>