VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 26 2014 - 10:13:20 CST

On Wed, Nov 26, 2014 at 10:36 AM, Rangeen Othman
<rangeen.othman_at_googlemail.com> wrote:
> Dear VMD Users,
>
> I have two structures (gold nano particle with lipid bilayer, pdb and psf
> files) I want to combine them using Psfgen but it failed! I wonder if
> someone will advise me what is the problem. Also I have checked that the
> system has unique {segname resid name}. I have also used Topotool to merge
> them but again it failed and complained with the same phrase!

there is not enough information here to give any advice, and i
seriously doubt that psfgen and topotools give the same error message
since they are completely different packages that don't share any
code.

axel.

>
> psfgen) reading coordinates from pdb file mergetmp1312235701/2nmfix2.1s.pdb
> psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A
> psfgen) Warning: failed to set coordinate for atom AU1 AU:2 A
> psfgen) Warning: failed to set coordinate for atom AU2 AU:3 A
> psfgen) Warning: failed to set coordinate for atom AU3 AU:4 A
> psfgen) Warning: failed to set coordinate for atom AU4 AU:5 A
> psfgen) Warning: failed to set coordinate for atom AU5 AU:6 A
> psfgen) Warning: failed to set coordinate for atom AU6 AU:7 A
> psfgen) Warning: failed to set coordinate for atom AU7 AU:8 A
> psfgen) Warning: failed to set coordinate for atom AU8 AU:9 A
> psfgen) Warning: failed to set coordinate for atom AU9 AU:10 A
> psfgen) Warning: failed to set coordinate for atom AU10 AU:11 A
> psfgen) Warning: failed to set coordinate for atom AU11 AU:12 A
> psfgen) Warning: failed to set coordinate for atom AU12 AU:13 A
> psfgen) Warning: failed to set coordinate for atom AU13 AU:14 A
> psfgen) Warning: failed to set coordinate for atom AU14 AU:15 A
> psfgen) Warning: failed to set coordinate for atom AU15 AU:16 A
> psfgen) Warning: failed to set coordinate for atom AU16 AU:17 A
> psfgen) Warning: failed to set coordinate for atom AU17 AU:18 A
> psfgen) Warning: failed to set coordinate for atom AU18 AU:19 A
> psfgen) Warning: failed to set coordinate for atom AU19 AU:20 A
>
> Thanks in advance
>
> Rangeen 

-- 
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.