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

[Tanping Li]

Dear Yang,

Really thanks for the help. Distance constraint can
describe the bond length between ligand and protein,
how about other propery of covalent bond? Maybe I
missed something of your message.

Yours
Tanping


--- Yang Ye <leafyoung at yahoo.com> wrote:

> 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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> 
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