Amir Abbasi wrote:
Hi!
I want to simulate an RNA molecule.
I have the .pdb file of that.
I want to create an Argon wall and make a hole on it to pull my molecule
through it.
Argon defined in OPLS/AA force field. but it has not nucleic acids.
how can i define the argon in other force fields?
http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
Simulations of argon have been done for many years. You may be able to find
suitable parameters by doing a literature search.
-Justin
--
========================================
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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