From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Nov 29 2004 - 17:01:33 CST
add a first none last none section to the DMV segment
On Mon, 29 Nov 2004, Hemant Kushwaha wrote:
> I want to simulate protein with ligand inside, the problem is while
> running psfgen it always add N and C terminal to the ligand which is
> wrong. Has anybody gone through this problem plz let me the solution
> of the problem, and also how can i generate psf file using psfgen with
> ligand inside the protein.
>
> my psfgen file is as follows:
>
> topology top_all27_prot_lipid.inp
> alias residue HIS HSE
> alias atom ILE CD1 CD
> segment U {
> pdb test_protein.pdb
> first ACE
> last CT3
> }
> coordpdb test_protein.pdb U
>
> segment DMV {pdb dmv_clean.pdb}
first none
last none
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
||||||||||||||||||||||||||||||||||||
> coordpdb dmv_clean.pdb DMV
>
> segment ION {pdb ion.pdb}
> coordpdb ion.pdb ION
>
> alias residue WAT TIP3
> segment SOLV {pdb water.pdb}
> coordpdb water.pdb SOLV
>
> guesscoord
>
> writepdb test.pdb
> writepsf test.psf
>
*****************************************************************
**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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