From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Feb 22 2013 - 00:49:17 CST
Hi,
I'm not using charmm, but what's about the messages psfgen gives you?
You should figure out why it doesn't know the residue you are going to use:
"unknown residue type PEG
failed!"
Make sure that you loaded parameter files that contain this residue, or make
sure that the name is correct.
Good luck
Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Titis Sekar Humani
> Gesendet: Freitag, 22. Februar 2013 07:05
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l:
>
> Dear all,
>
> I have some problem here. I got message on my terminal like I write
> bellow :
>
> psfgen) Created by CHARMM version 31 1
> psfgen) cross-term entries present in topology definitions
> psfgen) aliasing residue HIS to HSE
> psfgen) aliasing residue ILE atom CD1 to CD
> psfgen) aliasing residue HOH to TIP3
> psfgen) building segment U
> psfgen) setting patch for first residue to NONE
> psfgen) setting patch for last residue to NONE
> psfgen) reading residues from pdb file chainH.pdb
> psfgen) unknown residue type PEG
> psfgen) extracted 279 residues from pdb file
> psfgen) Info: generating structure...psfgen) unknown residue type PEG
> failed!
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
> vmd >
>
> Anybody could help me to resolve my problem?
> Thank you..
>
>
>
> Best regard,
> T.S. Humani
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