VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 01 2011 - 10:52:24 CDT

On Wed, Jun 1, 2011 at 11:17 AM, Mona Habibi <mhabibi2_at_uwo.ca> wrote:
>
>
> Hi,
> I have a single file in .gro  format and I want to change it to pqr format
> to do  some electrostatic analysis.
> I tried to write the file with exactly the same format of pqr , but VMD can
> not read my file in pqr format.(It can load the .gro format though)
> How can I change the format file to .pqr?

it is not only the format that is different, you also need to provide
the information about radius and charge, something that is not
present in a .gro.

the pqr plugin in VMD should be able to write out .pqr files.

please note, that it is difficult to discuss your problems without
seen some (small) example files.

axel.

>
>
> Regards,
> Mona Habibi
> Ph.D student
> Biological and Condensed Matter Physics Group,
> Dept. of Applied Mathematics, the University of Western Ontario,
> 1151 Richmond St. North, London (ON),  Canada N6A 5B7
> Email: mhabibi2_at_uwo.ca
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.