kala wrote:
Dear All,
I am planning to perform a simulation of a protein ternary complex with
2 ligands and Zn molecule. The protein has 2 chains with 430aa.Is it
possible to do simulation for the protein complex. I have got sufficient
hardware configuration for the dynamics study. As am new to perform such
complex simulations kindly help me to start with.
You can certainly simulate such a complex, but it may not be very easy. You
should start with basic tutorial material, including the tutorial about a
drug-enzyme complex to get yourself familiarized with proper topology organization.
http://www.gromacs.org/Documentation/Tutorials#General
Then, you should prepare yourself for the potentially arduous task of proper
ligand parameterization. This is an advanced topic, so be prepared to invest a
significant amount of time in getting ligand parameters right. This may be a
matter of weeks or months, if done properly. PRODRG is not sufficient for
generating reliable parameters, though this is not stated in the drug-enzyme
tutorial.
http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
The other complication is the Zn ion. Proper treatment of transition metals is
not trivial, and if this residue plays some important role in the function of
the protein, a standard MM treatment may not be appropriate. See the above
Parameterization page, particularly the Exotic Species section.
-Justin
kala bharath
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
