On Thu, Feb 13, 2014 at 8:27 AM, Rajeswari A.
<rajeswari.biotech.gmail.com>wrote:
> Dear Amber users,
> I simulate a protein ligand system. The ligand is an organic molecule and i
> calculated the ESP charge for the ligand using gaussian. After successful
> simulation, now i want to calculate mmgb(pb)sa decomposed energy. The
> ligand molecule is a single residue, however i want to split the ligand
> into multiple residues (suppose i want to split one methyl group as one
> residue and rest of the molecule another residue) and calculate the
> decomposition energy. Is there any way to do this?
>
You actually have to create two new residue templates with different names
that have the fragments you want. Then you have to change the PDB file so
each residue will have the appropriate name (and different residue numbers
from one another).
This will be more complicated than the current approach you used since the
two residues will need connectivity information (one residue will need a
HEAD atom and the other will need a TAIL).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 13 2014 - 08:00:03 PST
