VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Jul 21 2015 - 13:44:49 CDT

Just an FYI, this usually won't work particularly well unless the
proteins are well behaved. Usually there are missing pieces in pdb files
that need manual intervention. That being said, autopsf has a tcl interface:

package require autopsf
autopsf -mol top -top topologyfilehere

Check the other autopsf options to see if they might be useful to you.

-Josh Vermaas

On 07/21/2015 02:33 AM, Ashar Malik wrote:
>
> To start you off, make a list of all the pdb. Read them into a tcl
> script. Run a for loop for the number of pdb files you have and in
> each loop use the psfgen package.
>
> Try it. If you are still stuck .. Drop another email.
>
> On Jul 21, 2015 12:19 PM, "Akshay Bhatnagar"
> <akshaybhatnagar2790_at_gmail.com <mailto:akshaybhatnagar2790_at_gmail.com>>
> wrote:
>
> Hello everyone
>
> I have around 5000 proteins and i want to generate 5000 psf and
> subsequently generated pdb files for all these 5000 proteins in
> one shot. I have always use automatic psf generate method to
> generate psf. Now please anyone help in generating a tcl script
> through which i can generate all the 5000 psf and pdb files in one
> go using the script.
>
>
> With Regards
> Akshay Bhatnagar
> PhD Student
> BITS Pilani Hyderabad Campus
>