VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Aug 06 2013 - 17:45:18 CDT

Hi George,

The first part (making residue 42 a GLN) is fairly easy, and the mutator
plugin of VMD can get you to GLN without too much trouble. Adding on the
ethyl is somewhat more complicated. In principle, the correct thing to
do is to:

1.) Make a patch to add the ethyl to GLN (look at PRES residues in
CHARMM topology files for an example of what these look like, and the
psfgen user guide on how to apply them)
2.) Apply the patch to your system, check your parameters.
3.) Run simulations and be happy.

The difficulty lies in making sure parts of the structure like the
atomic charges, bonds, angles, and dihedrals are setup properly, as the
OPLS force field and the CHARMM force field are parameterized
differently, and use slightly different forms for their Lennard Jones
potentials. Thus, it may not be easy or correct to combine the existing
OPLS parameters with CHARMM. Depending on what the rest of your
simulation system looks like, it may just be easier to switch the whole
system over to using OPLS parameters and use those during simulation
instead of the more widely used CHARMM parameters. Building a structure
meant to be used with OPLS parameters should not be any more difficult
(your topology file is now top_opls_aa.inp instead of top_all36_*.rtf,
and your patch will differ accordingly), but will take some
understanding to get right with psfgen.

Good luck!
-Josh Vermaas

On 08/06/2013 03:06 PM, George Omolloh wrote:
> I am a newbie to VMD and NAMD and need to mutate a residue in my
> protein say residue 42 GLU to a nonstandard 42 GLN, with the
> sidechain N having an extra ethyl group (-NH-CH2-CH3) before I
> continue with my molecular dynamics. The parameters to these extra
> atoms are also in the OPLS forcefield. How do I perform this type of
> mutation.
> Thanks,
>
> George O. Omolloh
> Research Assistant - Prof. Gascon's Lab,
> University of Connecticut
>
>