Travis Craddock wrote:
Hello,
I am a new GROMACS user. My aim is to simulate the protein tubulin with a GTP
molecule present. When attempting to create a topology file I receive a Fatal
Error stating that the "Residue GTP is not found in the topology database". I
understand that GTP is not parameterized for the force field that I am using,
and from what I have read of previous posts, creating a new *.itp file is
rather complicated and not recommended for new users. As such, I would like
to ask if anyone can recommend a starting point to learn more about
simulations in GROMACS so that I can eventually learn how to run my intended
simulation, i.e. tutorials dealing with the creation of *.itp files, or
previous work that outlines some of the details. Thank-you.
Doing a simple Google search for "Gromacs tutorial" should yield some
good results. Take a look at the wiki site as well, there's lots of
information there.
Creation of .itp files will require thorough knowledge of how the
original force field was derived, and then applying that procedure to
your molecule. Parameters for GTP under Gromos96 were discussed across
this list not too long ago (search the archive), and if you're using
Amber, you can use tools to create a GAFF-parameterized molecule using
antechamber and convert it to .itp format using tools available in the
User Contributions on the Gromacs site.
-Justin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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