VMD-L Mailing List

From: Sunjoo Lee (sunnytov_at_gmail.com)
Date: Wed Oct 07 2009 - 12:17:12 CDT

Hi
Or you can generate the connectivity (bonding) information and put the
information at the end of pdb file.
It is the simplest way to generate the bond for CG molecules.

Cheers,
Sunjoo

On Wed, Oct 7, 2009 at 9:39 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, Oct 7, 2009 at 3:21 AM, Baofu Qiao <qiaobf_at_gmail.com> wrote:
> > Hi Young-Min,
> >
> > Have you found some way to show the bonds in coarse grained model? Now I
> > meet the same problem.
>
> have you tried the top2psf script as i suggested in reply to the original
> mail?
> n.b.: you have to use a top file that is generated _while_ generating your
> .tpr
> file by giving the -pp option to grompp.
>
> axel.
>
>
> > best regards,
> > Baofu Qiao
> >
> > BAN,YOUNG MIN wrote:
> >> Hello.
> >>
> >> I am trying to represent DPPC lipids as bonds or lines. But since I am
> >> using Marrink's coarse grained model, it seems that vmd does not
> >> recognize bonding between coarse grained molecules. I am using
> >> Gromacs, so I have .gro, .itp, and .top files.
> >>
> >> How can the lipids be represented by bonds or lines using those .gro,
> >> .itp, or .top files? Do I need other type of files to do this?
> >>
> >> Thanks in advance.
> >>
> >> Young-Min Ban
> >>
> >>
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>