[gmx-users] MD simulations of covalent bound protein-ligand complex by gromacs

[Justin A. Lemkul]

On 4/26/12 10:23 AM, mircial at sjtu.edu.cn wrote:
> Dear All:
>
> I am simulating a complex of protein and ligand, however, the ligand is
> covalent bound to the protein. I have calculated the charges of the ligand
> and the non-standard residue by QM method and trying to use the bond
> parameters in the GROMOS force field. However, I don't know how to made the
> topology file of the complex, do I need to change the topology file manually
> to add the necessary things?
>

Let pdb2gmx do all the work for you:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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