In addition to what Justin has said there are parameters for GTP to use
with the amber forcefields, see:
http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
Obviously you need to convert these from an amber format to a gromacs one.
Do note that an additional atom type for the terminal anionic oxygens is
needed so the conversion using the contributed tools may not be straight
forward
Tom
--On Wednesday, June 25, 2008 13:57:23 -0400 "Justin A. Lemkul"
<[EMAIL PROTECTED]> wrote:
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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----------------------
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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