Re: the patch between segments for multiple chains molecule.

From: Moumita Maiti (
Date: Wed Jun 14 2006 - 06:21:09 CDT


           I used the following format to link two nucleic acid residues.

"patch LKNA dn1 FIRS dn1 LAST". It gives the error

"applying patch LKNA to 4 residues
ERROR: resid missing from patch target DN1
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over."

In addition I get an error for disulphide "DISU" patch,

"applying patch DISU to 1 residues
ERROR: failed to apply patch"

Is there a manual where I'll get all the required formats to create a psf
file for a multichain molecule?

Thank you,

On 6/2/06, Leonardo G. Trabuco <> wrote:
> On Fri, Jun 02, 2006 at 10:44:58PM +0530, Moumita Maiti wrote:
> > Hi,
> >
> > I think I have to add a patch between two segments in the
> case
> > of the multiple chains and for dna, so I get the
> > warnings there, I have attached the file which generates psf file. Iget
> some
> > warnings also when I run this with vmd.
> If the chains are not covalently linked, you shouldn't need to add a
> patch. Otherwise, the patch to link two nucleic acid segnments is LKNA.
> > Can you please send me an example file or tell me where I should modify
> > the file 1kx5.pgn to add these pathces.
> If you look at the CHARMM topology file, you're going to see that the
> residues ADE, CYT, THY, and GUA correspond to ribonucleobases. You
> probably want to add a patch to eliminate the 2'-OH group. There are two
> patches for that, one for pyrimidines (DEO1) and the other for purines
> (DEO2). You have to apply such a patch for each residue in your DNA
> molecule.
> Best,
> Leo
> --
> Leonardo Giantini Trabuco
> Ph.D. candidate
> Center for Biophysics and Computational Biology
> University of Illinois at Urbana-Champaign

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