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

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

Dear Gromacs-Users,

I want to do a MD with implicit solvent.
During this I'll get the following erros.

		GB parameter(s) missing or negative for atom type 'ca'

		GB parameter(s) missing or negative for atom type 'OS'

		GB parameter(s) missing or negative for atom type 'nh'

		GB parameter(s) missing or negative for atom type 'c3'

		GB parameter(s) missing or negative for atom type 'ha'

		GB parameter(s) missing or negative for atom type 'hn'

		GB parameter(s) missing or negative for atom type 'h1'

		GB parameter(s) missing or negative for atom type 'h4'

		GB parameter(s) missing or negative for atom type 'OW_spc'

		GB parameter(s) missing or negative for atom type 'HW_spc'

		GB parameter(s) missing or negative for atom type 'Na'

		GB parameter(s) missing or negative for atom type 'Cl'


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?

Thanks for your help in advance.

Best regards,

German
-- 
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