On Mon, Oct 14, 2002, Nicolas Le Novere wrote:
>
> I am sure my query is a common one among newbies, and in such a case I
> apologize for the inconvenience. I am modelling a protein with several
> disulfide bonds. The original PDB has been generated by MODELLER, so I
> renammed CYS into CYX, and suppressed the inaccurate HG.
>
> Nevertheless, any manipulation with sander, like a minimization or an
> equilibration cause my disulfide bonds to disappear, and therefore each
> sulfur to move away.
>
> tleap session:
> -------------
>
> > a7 = loadPDB a7gg.pdb
> Loading PDB file: ./a7gg.pdb
> > solvateBox a7 WATBOX216 { 36 18 25 } 25
It's not enough to just change CYS to CYX. You also have to use the
"bond" command in leap to add the S-S bonds. See, e.g. the bpti tutorial
on p. 14 of the Users' Manual.
.good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Mon Oct 14 2002 - 09:04:30 PDT
