* Mark Abraham; Montag, den 02. Apr 2012 > On 2/04/2012 7:57 PM, german.erlenk...@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.erlenk...@pharmazie.uni-halle.de Phone: (49)345 - 55 25 194 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
