[gmx-users] Protein-ligand

Justin A. Lemkul jalemkul at vt.edu
Wed Dec 23 19:55:21 CET 2009

Quoting "P.R.Anand Narayanan" <nandu_cooldevil at yahoo.co.in>:

> Dear Gromacs users,
> I am planning to bind a ligand to a protein and use gromacs to run the
> simulations. But for using the pdb2gmx command, i heard we have to remove all
> the ligands and cofactors associated with the protein. While pasting the
> necessary parts of the ligand into the gro file, i heard that the bonds would
> be broken. Is this true? and if yes are there methods to run the pdb2gmx
> command with the ligand. Or the same command without the ligand but not
> breaking the bond after pasting it back.
> Pls help

There is a tutorial on the Gromacs site for protein-ligand simulations.  I
suggest you look through it.  If your ligand is covalently bound, you have an
entirely different (and somewhat more difficult) issue.


> Anand
>       The INTERNET now has a personality. YOURS! See your Yahoo! Homepage.
> http://in.yahoo.com/


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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