[gmx-users] Adding Born Radii for implicit solvent MD

[german.erlenkamp at pharmazie.uni-halle.de]

* Mark Abraham; Montag, den 02. Apr 2012
> On 2/04/2012 7:57 PM, german.erlenkamp at pharmazie.uni-halle.de wrote:
> > Dear Gromacs-Users,
> >
> > I want to do a MD with implicit solvent.
> >
> >
> >
> > It seems that I have to add the Born-Radii for these atoms.
> > I have the Radii, but I don't know where I have to add them neither
> > what will be the right syntax.
> >
> > Do I have to add the information in the itp-file for the ligand, the
> > complex or in gbsa.itp?
> 
> See manual 5.3.5. The lookup is done by atomtype, so the best approach 
> is to make a local copy of the whole forcefield directory to your 
> working directory, modify probably gbsa.itp. pdb2gmx will (be able to) 
> pick up the local copy when generating the .top, so that grompp will 
> find the parameters later.

Thanks, it worked for me.


-- 
German Erlenkamp
Institut fuer Pharmazeutische Chemie
Martin-Luther-Universitaet Halle	
Wolfgang-Langenbeck-Str.4
06120 Halle/ Saale

E-Mail:	german.erlenkamp at pharmazie.uni-halle.de
Phone: (49)345 - 55 25 194