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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--
========================================
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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