From: Peter Freddolino (
Date: Tue Jul 17 2018 - 08:00:32 CDT

Dear Matina,
It would be helpful to paste the error output that you get from VMD when
you try to run this. Chances are it is having trouble with your topology
file, but without more information it is impossible to guess what is going

On Tue, Jul 17, 2018 at 4:59 AM, Stamatia Zavitsanou <> wrote:

> Hello,
> I am trying to generate a PSF file in order to run a NAMD/FEP simulation.
> I use input from CGenFF.
> I have created the dual topology file (hybrid.rtf which is created after I
> have merged the reference with the mutant ligand into one file) and the
> complex.pdb file of the protein and the two ligands.
> I want to use autopsf and I load the complex.pdb file, the topology of the
> two ligands, hybrid.rtf file and these two files that I have found from
> CGenFF, toppar_water_ions_namd.str, top_all36_cgenff.rtf. Is this correct?
> It only creates a complex007_autopsf-temp.pdb not a final I think it's
> because VMD cannot read my hybrid.rtf file. Has anyone tried to do anything
> like that?
> If not how do you create the PSF file to run a NAMD/FEP simulation?
> Thank you,
> Matina