Re: make psf error for ligand

From: Oscar Bastidas (
Date: Wed Aug 23 2017 - 17:59:27 CDT

Hi Natasha,

For "HIS to HSE" error, did you change the histidine names in your pdb file
from HIS to HSE? Doing so should alleviate that problem. It's the same
situation with re-naming isoleucine's CD1 to CD in the pdb file with
respect to the second error. I hope this helps.


Oscar Bastidas, Ph.D.
Virginia Commonwealth University
Chemical and Life Science Engineering
On Aug 23, 2017 5:51 PM, "Natasha Gupta" <> wrote:

> Hi,
> I am trying to create a ligand from pdb structure from RCSB and parameters
> via paramchem. I am seeing the following error:
> psfgen) aliasing residue HIS to HSE
> psfgen) aliasing residue ILE atom CD1 to CD
> psfgen) building segment A
> psfgen) reading residues from pdb file A.pdb
> psfgen) extracted 1 residues from pdb file
> psfgen) setting patch for first residue to NNEU
> psfgen) setting patch for last residue to CNEU
> psfgen) Info: generating structure...psfgen) unknown patch type CNEU
> failed!
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> Any ideas on how to troubleshoot?

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