From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Dec 03 2003 - 14:30:29 CST
Hi
In the segement command for the dna segment add
first none
last none
This should stop the terminal patching of the DNA segment.
Brian
On Wed, 3 Dec 2003, David E. Konerding wrote:
> Hi,
>
> I am attempting to make a psf containing a protein bound to a DNA duplex
> so I can simulate it in NAMD (the model is derived from 1A31.pdb and
> 1A35.pdb).
>
> unfortunately, the manual doesn't give much guidance in building
> protein/dna PSF, here's what I did: first I split the PDB chains into
> distinct files, and
> massaged atom names and residue types to make psfgen happy with them. I
> can write .psfgen scripts which work to make each chain into a distinct PSF
> but I can't get the whole one, because, apparently, psfgen wants to
> apply the default NTER and CTER patches to the DNA terminii.
>
> Here's a couple examples of working individual psfgen input:
>
> ##Protein
> topology top_all27_prot_na.inp
> alias residue HIS HSD
> alias atom ILE CD1 CD
> alias atom PHE OXT OT1
> segment topoI { pdb topoI.pdb }
> coordpdb topoI.pdb topoI
> guesscoord
> writepdb topoI.pdb
> writepsf topoI.psf
>
> ##DNA chain C
> topology top_all27_na.inp
> alias residue A ADE
> alias residue G GUA
> alias residue C CYT
> alias residue T THY
> segment dnaC { pdb dnaC.pdb }
> coordpdb dnaC.pdb dnaC
> guesscoord
> writepdb dnaC.psf.pdb
> writepsf dnaC.psf
>
>
> Note: I had to use the top_all27_na.inp to work with DNA, otherwise, it
> applies the default amino acid terminal patch.
>
> When I combine these into a single script, I have to select one topology
> file or another; I picked top_all27_prot_na, since that seems
> to have both proteins and nucleic acids, which would be necessary for my
> mixed system.
> Byut that's the input file that causes the DNA terminii to be patched.
>
> I looked pretty extensively in the NAMD manual but it wasn't illuminative.
>
> Thanks,
> Dave
>
>
>
-- ***************************************************************** **Brian Bennion, Ph.D. ** **Computational and Systems Biology Division ** **Biology and Biotechnology Research Program ** **Lawrence Livermore National Laboratory ** **P.O. Box 808, L-448 bennion1_at_llnl.gov ** **7000 East Avenue phone: (925) 422-5722 ** **Livermore, CA 94550 fax: (925) 424-6605 ** *****************************************************************
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