[gmx-users] Dealing with residues not in the topology database

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 25 19:57:23 CEST 2008

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.


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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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