VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 23 2012 - 14:12:02 CDT

Hi,
  Can you email me your .gro file that causes problems? I can probably
fix the .gro reader plugin if I have a few known-valid input files that
have the issue you describe below.

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. 

-- 
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