[gmx-users] constraint distance between ligand and protein

David Mobley dmobley at gmail.com
Wed Sep 13 17:15:08 CEST 2006


On 9/11/06, kanin wichapong <kwichapong at gmail.com> wrote:
> Hi All,
>     I would like to know how to make a distance constraint between the
> ligand and the protein. If I just merge two chain together by pdb2gmx, it
> can done if the two chain are both protein. However, if it is a ligand and
> protein, i can't merge together because there is no libraly for the ligand
> force field and then it can't generate the .itp or .top file

You need a script to do this, as there's no built-in way to do it. I'm
assuming you DO already have top and gro files for the ligand, though?

If so, I have a script I use to do this for my ligand/proteins... With
a bit of modification you could probably make it work for you. E-mail
me off list if interested.


> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list