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

[Mark Abraham]

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.
> 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?

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.

Mrak