How to convert gromacs' force field file format to pdb2pqr (.DAT and .names) format?

03 March 2018 1 829 Report

Hi.

I need to use pdb2pqr in a molecule that I am studying but it does not have the GROMOS53a6 force field available. I know that there is an option to add a force field but it has to be in a specific format (.DAT and .names). I understand the .DAT file structure and download the GROMOS53a6 force field from gromacs website but I cannot manage to convert from one to another because I could not find the radius of each atom in the GROMOS53a6 files. Does anyone could help me with it?

Thanks in advance.

Biswajit Sadhu

Dear Ronald,

Autodock software can convert pdb files into pdb2pqr format. Please follow the following link for more details:

http://autodock.scripps.edu/resources

Regards,

Biswajit

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