On 5/2/12 6:55 AM, Hagit G wrote:
Hi gmx users,
Well, I saw this question but the answer was not understood.
I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with a
disulfide bond. Gromacs automatically adds H atoms.
Although the disulfide bond is there, Gromacs ignore it because *each cystein is
on a different chain*. So it adds H and therefor the disulfide bond is ruined
during energy minimization.
Is there any way to recreate such a disulfide bond (Please don't tell me again
about "-ss" it works only on one chain. Moreover, the bond is existed on the pdf
file.) or never ruined it at the first place?
Well you may need to use -ss, but since you don't want to hear about it, I won't
say anything more...
What you need to do is create a [moleculetype] that consists of both chains.
The pdb2gmx option -chainsep will allow you to create a properly merged molecule
that can form the intermolecular disulfide because the two molecules will be
considered as one [moleculetype], as Gromacs requires.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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