[gmx-users] Problem with the simulation of C2160 (fullerene)

[Justin Lemkul]

On 4/23/13 1:31 AM, jhon michael espinosa duran wrote:
> Hi guys
>
> I have a problem with the MD simulation of C2160 (Fullerene)
> with doxorubicin molecules inside. I have a OPLS force field
> for C60 that I am using for C2160, and for Doxorubicin, I generate
> the force field using PRODRG.
> The problem is that PRODRG is based on Gromacs so the two structures
> are based on different force fields.
>

Make sure you get the nomenclature right here - it is not based on "Gromacs," 
the parameters it gives you are based on Gromos96 43A1.  The fact of the matter 
is those parameters are very poor and require manual refinement (see 
http://pubs.acs.org/doi/abs/10.1021/ci100335w).

> What can I do to fix the problem?
> I can change the drug if it is necessary, any drug avaliable in OPLS?
>

You need to choose a force field that can adequately describe all species.  You 
can't mix and match.  Most drugs and small molecules are not built in to 
existing force fields, which are generally only designed for proteins, nucleic 
acids, and some lipids.  Common cofactors typically exist in most force fields, 
but not many other molecules unless someone has published parameters for them.

-Justin

-- 
========================================

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

========================================