[gmx-users] PEO and OPLS-AA FF in gmx

[Justin A. Lemkul]

lammps lammps wrote:
> Hi,
>  
> I want to simulate a PEO chain in water using OPLs-AA FF in Gromacs.
>  
> I have created a .PDB file using Material Studio, but I seems that the 
> pdb2gmx can not dealt with it because of the error" Residue 'xx' not 
> found in residue topology database"
> The question is how can I obtain the .top and .gro file in the framework 
> of OPLS-AA FF. Any suggestion is appreciated.
>  

You have to derive parameters for yourself:

http://www.gromacs.org/Documentation/How-tos/Parametrization

There are a few scripts in the User Contributions section that make efforts to 
do this for you, but you still have to demonstrate that the parameters are valid.

-Justin

> Thanks in advance.
> 
> -- 
> wende
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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