[gmx-users] Re: Simulation with CsCl

[Justin A. Lemkul]

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 /<vvchaban at gmail.com>/* wrote:
> 
> 
>     From: Vitaly Chaban <vvchaban at gmail.com>
>     Subject: [gmx-users] Re: Simulation with CsCl
>     To: gmx-users at gromacs.org
>     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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