[gmx-users] Help: A ligand covalently bond to protein

Yang Ye leafyoung at yahoo.com
Tue Nov 6 22:39:35 CET 2007

you might want to try distance constraint.

On 11/7/2007 5:11 AM, Tanping Li wrote:
> Dear all,
> I searched the mailling list, and still can't find a
> way to set up my system: a ligand covalently bond to
> protein.
> I don't know if there is a easier way to do this. What
> I can think of is:
> 1) Add a bond I like in the specbond.dat file;
> 2) Add a block for ligand in the rtp file;
> 3) run pdb2gmx, gromacs will treat protein and ligand
> a one chain since it can see the bond in the
> specbond.dat.
> I just wonder if there is a eaiser way to add a ligand
> to rtp file? When I run Dundee PRODRG2, I get a .itp
> file. Is there some way to change this into rtp
> format? It is not trival to write a rtp manually.
> Really appretiate your help.
> Yours
> Tanping
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