Re: the patch between segments for multiple chains molecule.

From: Leonardo G. Trabuco (
Date: Fri Jun 02 2006 - 13:09:23 CDT

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


Leonardo Giantini Trabuco
Ph.D. candidate
Center for Biophysics and Computational Biology
University of Illinois at Urbana-Champaign

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