AMBER Archive (2002)

Subject: Re: loss of disulfide bonds

From: David A. Case (case_at_scripps.edu)
Date: Mon Oct 14 2002 - 11:04:30 CDT

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 

-- 

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