From: Mayne, Christopher G (
Date: Wed Oct 21 2015 - 14:44:18 CDT


I have found that the best way for generating a PSF file of small molecules from coordinates is to use the TopoTools API. There is extensive documentation on Axel’s website (

Christopher Mayne

On Oct 21, 2015, at 11:40 AM, Nikhil Maroli <<>> wrote:

Dear users,
i want to do MD of protein and drugs together after docking,i done the docking part now when i try to create psf file there is topology problem so anyone can tell me how to solve this problem-how to get the topology parameter for drugs ?
Thanks in advance

Nikhil Maroli