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.
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
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