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

[Tanping Li]

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