How can I convert an enzyme pdb file into a topology file for GROMACS use?

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Ranylson Marcello Leal Savedra

Dear Manoj,

use the tool pdb2gmx (GROMACS). I have attached a website to illustrate how to use this tool.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html

Meenu Sharma

its a wonderful turorial. thanks.

but prodrg server is not working now a days. is there any other option to convert ligand coordinates from pdb to gro format.

Aykut Elmas

how about pdb to moltemplate topology file? ATB web page doesnt let me for molecules that contains more than 1000 atoms