Re: the patch between segments for multiple chains molecule.

From: Leonardo G. Trabuco (
Date: Wed Jun 14 2006 - 12:57:42 CDT

On Wed, Jun 14, 2006 at 04:53:04PM +0530, Moumita Maiti wrote:
> Hi,

Hi Moumita,

> 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."

The syntax is patch LKNA dn1:FIRST dn1:LAST

where dn1 is your segname (you can, of course, link between different
segments). I assume FIRST and LAST will work in this case, but if
doesn't, try using the residue number instead.
> In addition I get an error for disulphide "DISU" patch,
> "applying patch DISU to 1 residues
> ERROR: failed to apply patch"

By the error, it seems that you're trying to apply the patch to only 1
residue, but you should be applying it to two residues. It's probably a
syntax error, it should read pretty much as the above patch.

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

There's an example in the psfgen userguide, but it's quite simple, you
just have to have one "segment" and one "coordpdb" entry for each chain
(no need to patch or anything). Now, if you want to add a covalent bond
between two segments, you'll need a patch (like you're trying to do with
the LKNA above).

Hope this helps,

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

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