VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Aug 30 2014 - 11:21:33 CDT

On Sat, Aug 30, 2014 at 5:14 PM, sunyeping <sunyeping_at_aliyun.com> wrote:
> Dear all,
>
> In VMD script library there is a script c_top2psf.pl. This is to transform
> top file into psf file.
>
> I used this command line to do the transformation:
>
> perl c_top2psf.pl -p topol.gro -o topol.psf
>
> However, the only content of the psf it generated is:
>
> PSF
> 4 !NTITLE
> REMARKS TOPOLOGY CREATED BY PERL SCRIPT (MARC BAADEN)
> REMARKS contact baaden smplinux.de
>
> 0 !NATOM
>
> 0 !NBOND: bonds
>
> Maybe I misused this script. Could you tell me how I can get a normal psf
> file which contains the atom cooridnations?

a) you use a .gro file and not a topology file. you need a _complete_
topology file without any includes and preprocessor directives.
b) a .psf file contains no coordinates.

>
> Best regards.
>
>
>
>
> Yeping 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.