VMD-L Mailing List

From: Rangeen Othman (rangeen.othman_at_googlemail.com)
Date: Wed Nov 26 2014 - 11:09:20 CST

Thanks for the reply, I want to merge both structures but it complained
about failed set of coordinates For example; "psfgen) Warning: failed to
set coordinate for atom AU31 AU:319 A". I have also used "
 vmd>>extensions>>modeling>>merge structures " again gives me the same
warning! I have checked the merged pdb all coordinates of Au atoms are (0,
0, 0)! I have used also topotools it worked and combined them, however,
when I wanted to delete some water around gold nanoparticle it failed again
because of using psfgen to do that!

Thanks a lot

Rangeen

On Wed, Nov 26, 2014 at 4:13 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>