VMD-L Mailing List

From: satya kumar (mail2mvskumar_at_gmail.com)
Date: Tue Jul 24 2012 - 06:49:55 CDT

Hello Bogdan,

Thanks for your reply.

I used fixed GROMACS fixed file format. In the coordinate columns, if you
have more than 4 digits before the decimal point, then you get into issue.
For validation purpose, I had rechecked this even in VMD by selecting that
particular residue and it turned out that VMD takes in only 3 digits before
the decimal.

Thanks,
Satya.

On Tue, Jul 24, 2012 at 5:02 AM, Bogdan Costescu <bcostescu_at_gmail.com>wrote:

> Hi!
>
> Both the PDB and GRO file formats use a fixed-column format. It's not
> the VMD plugin reader but the file which is faulty. The GRO format (at
> least as produced by GROMACS) didn't change recently, so there's no
> reason to change the plugin reader which worked fine so far.
>
> Cheers,
> Bogdan
>
> On Mon, Jul 23, 2012 at 7:24 PM, satya kumar <mail2mvskumar_at_gmail.com>
> 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.
>