[gmx-users] constraint distance between ligand and protein

[David Mobley]

Kanin,

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.

David

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