parthi...@ncbs.res.in wrote:
Message: 3
Date: Thu, 20 Jan 2011 09:30:00 +0000
From: Oliver Grant <olivercgr...@gmail.com>
Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
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Show us that part of your topology. When you used ffamberports have you
renamed the CYS to CYS2?
Oliver
could you explain this in detail where this change have to done.? i can
check again.
If the disulfide was created by pdb2gmx, then specbond.dat will have done this
for you and assigned the proper parameters. Did pdb2gmx automatically assign
your bond for you, or did you make post-pdb2gmx manual changes to your topology?
-Justin
------------------------------
Message: 4
Date: Thu, 20 Jan 2011 20:54:39 +1100
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <7690be842aff.4d38a...@anu.edu.au>
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parthi...@ncbs.res.in wrote:
Hi
I am using a dimer for my simulation system which is connected by 2
disulfide bonds.
After energy minimization for even few cycles, the disulfide bond
breaks
which is not expected.
Bonds do not break in classical molecular mechanics. One of two
things is
happening:
1. There was never a bond to begin with (check your topology)
There do a bond exists.
So you can see in your [bonds] section an entry for the two atom numbers?
I cant see any corresponding entry with res.to CYS residues.
2. The bond is highly strained, in which case something is wrong with
your
structure.
i have applied amber99 force field and prepared the system. while i
tried
with another force field in Gromacs which did not worked at all.
What does that mean? What failed?
As said previously the bond is strained only after pdb2gmx itself. is
there any other way to fix it.
Previously you said the bond was strained after EM. pdb2gmx is not capable
of straining a bond.
Be sure you are not looking at "bonds" generated via heuristics in some
visualization program. If pdb2gmx is generating a disulfide bond, it will
say so in the standard output, and you will be able to find it in the
[bonds] section. Otherwise, there is no bond.
Mark
I used pymol and vmd to visualize this
Thanks
Parthiban.
--
========================================
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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