From: Vermaas, Joshua (
Date: Thu Jun 29 2017 - 16:02:22 CDT

Hi Mary,

Comment it out, but only after understanding what the command was supposed to do. You can comment it out if you have psfgen autogenerate statements (regenerate angles dihedrals) in your script right before writing the psf, since then psfgen will rebuild the angles and dihedrals from bonds anyway, which is what "auto" is supposed to do. The "patch" syntax is a new CHARMM feature that psfgen can't parse yet. If you read the CHARMM documentation (, you see that the extra "patch" statement is there to tell CHARMM to not be dumb and automatically generate angles and dihedrals after patches get applied. So to be super clear, what you should have is something like:

topology ...
segment {
#Do more stuff here

regenerate angles dihedrals
writepsf output.psf
writepdb output.pdb


On 06/29/2017 02:53 PM, Ashar Malik wrote:
Comment it out.

On Jun 30, 2017 07:18, "Mary Lowe" <<>> wrote:

I have the same question as the one posted on June 6, 2016 by Gupta. The CHARMM36 topology files contains the command AUTO ANGLES DIHE PATCH. When I read this topology file using psfgen in VMD, it gives the following error:

ERROR: Failed to parse autogenerate statement

Can I replace the command with AUTO ANGLES DIHE? Can I comment out the command?