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

Travis Craddock tcraddoc at phys.ualberta.ca
Wed Jun 25 17:59:58 CEST 2008


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.

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