sonali dhindwal wrote:
Hello All ,
I am also trying to simulate my protein with Mn ion present in it.
So can I create the topology entry for Mn ion similar to MG2+ ion ? and
how can I get the values of C6 and C12 leonard jones potential in [atom
type] entry and will it be required to add [nonbond_params] also ? how
can I get them ?
Also I want to use Fe2+ also, but it is also not included in gromos
force field. This problem of adding other ions and molecule in the
system always remains. And being new to this field, can someone suggest
in simple terms how to include these considering the person is not an
expert in this field.
Please consult the link I posted yesterday...
http://www.gromacs.org/Documentation/How-tos/Parameterization
What you're trying to do is far from trivial. Understand that parameterization,
especially for transition metals, is very challenging, and standard molecular
mechanics treatment of such species suffers from many limitations, which may or
may not influence your results.
-Justin
Please help.
--
Sonali Dhindwal
--- On *Tue, 8/6/10, Vitaly Chaban /<[email protected]>/* wrote:
From: Vitaly Chaban <[email protected]>
Subject: [gmx-users] Re: Simulation with CsCl
To: [email protected]
Date: Tuesday, 8 June, 2010, 9:03 PM
> Hi all:
> I am trying to simulate a polysaccharide in solution of water and
CsCl, but
> cesium is not parametrized in the gromacs 4. I am using the force
> field GROMOS 96.
> I have looked for the parameters of Cs+ in the OPLS Force field
and I have
> created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I have
include
> the parameters for Cs+ in the "ions.itp" file, but it didn't
work, Can
> someone help me?
> Thanks in advance.
> Cecilia.
Cecilia -
You do not need so many files so cesium. Just copy your parameters to
the force field used and create the topology entry for cesium similar
to
[ moleculetype ]
Ar 1
[ atoms ]
1 Ar 1 Ar Ar 0 0.0
Do not forget, cesium+ is an ion...
--
Dr. Vitaly Chaban
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--
========================================
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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