Re: patch DISU to 2 residues

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Wed Dec 17 2008 - 12:13:20 CST

When building the PSF, you can define an arbitrary segment of your
protein - in this case you would have to declare it as Segment A
containing the relevant residues (likely the entire protein or domain
you are interested in), build it using PSFgen, and then apply the
patch. It can all be done in the same script.

-Eric

On Dec 17, 2008, at 11:58 AM, jose correa wrote:

>
> Dear NAMD's users
>
> I have a protein that have one bond Cys-Cys, so, I need to add:
> patch DISU A:131 A:215
>
> but, after run the psfgen, its output shows:
>
> Created by CHARMM version 27 1
> aliasing residue HIS to HSD
> aliasing residue ILE atom CD1 to CD
> applying patch DISU to 2 residues
> no segment A
> ERROR: failed to apply patch
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
> Can you help me?
> Best wishes
>
> Jose Correa-Basurto
> ESM-IPN, Mexico

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

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