VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 31 2012 - 11:23:19 CDT

Hi,
  I have rewritten portions of the VMD Gromacs plugin to address this
problem. I will have a new test version of VMD posted this afternoon
that contains the new version of the Gromacs plugin that you can try out
by downloading it from the VMD BioFS "alpha" directory described here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jul 23, 2012 at 01:24:20PM -0400, satya kumar wrote:
> Thanks for the reply.
>
> I tried converting ,gro to .pdb format. I tried to view in VMD but the Z
> coordinate is creating an issue again. In .pdb format we have:
>
> ATOM 5231 OW OHX 2171 -5.430 -25.80010000.000 1.00
> 0.00
> ATOM 5232 HW1 OHX 2171 -5.100 -25.47010001.100 1.00
> 0.00
>
> Instead of reading Z coordinate as 1000 and 10001.100, VMD is reading them
> as 000 and 0001.100. Probably there should be a white space between
> successive columns.
>
> With Regards,
> Satya.
>
> On Mon, Jul 23, 2012 at 12:46 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
>
> On Mon, Jul 23, 2012 at 5:06 AM, satya kumar <mail2mvskumar_at_gmail.com>
> wrote:
> > Hello All,
> >
> > I am a VMD user, experiencing an issue with reading coordinates in VMD
> from
> > a Gromacs file. Sample coordinate from GRO file is:
> >
> > 1OHX OW 5231 -0.543 -2.5801000.000
> > 1OHX HW1 5232 -0.510 -2.5471000.110
> >
> > where the "position (in nm, x y z in 3 columns, each 8 positions with
> 3
> > decimal places)". {X,Y,Z} = {-0.543, -2.580, 1000.00} and {X,Y,Z} =
> {-0.510,
> > -2.547, 1000.110}. When we view in VMD, these numbers are multiplied
> with a
> > factor 10 to convert to Angstrom, then in particular Z coordinates are
> > converted to 000 and 0.110 respectively. In VMD the above coordinates
> taken
> > as:
> >
> > {-5.429999828338623 -25.801000595092773 0.0}
> > {-5.099999904632568 -25.47100067138672 1.100000023841858}
> >
> > These create problems with respect to analysis, in particular the Z
> > coordinate. Can someone guide me to fix this issue.
>
> you have to fix the gromacs plugin reader to not use
> a simple scanf() call to parse coordinates in .gro files,
> but split the columns first and then parse the numbers.
> same as the .pdb molfile plugin does.
>
> ... or you simply use a (different) file format where
> these issues don't show.
>
> axel.
>
> >
> > Thanks,
> > Satya.
> >
> >
> >
> >
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078