VMD-L Mailing List

From: Sourav Ray (souravray90_at_gmail.com)
Date: Sat May 07 2016 - 10:40:24 CDT

Hello

I guess you will need topology file for nucleic acid too, check the
topology files in latest version of CHARMM.

Regards
Sourav

On Sat, May 7, 2016 at 8:13 PM, Roshan Shrestha <roshanpra_at_gmail.com> wrote:

>
> Hi,
>
> I am newbie in VMD and NAMD. Since I am finding it a bit difficult to
> use Automatic psf builder, I am instead using scripting at TK console to
> prepare psf for my pdb. I took a small protein BPTI (6pti.pdb) and trying
> to create psf for this protein. When I typed segment BPTI {pdb 6pti.pdb}
> after topology top_all22_prot.inp, I ran into the error
> Info: generating structure...psfgen) unknown residue type PO4
> failed!
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR!
>
> What the reason behind this error and how can I overcome it? Thanks
>