VMD-L Mailing List

From: Bogdan Costescu (bcostescu_at_gmail.com)
Date: Tue Jul 24 2012 - 04:02:59 CDT

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.