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

[TJ Piggot]

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" 
<jalemkul at vt.edu> 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
t.piggot at bristol.ac.uk
University of Bristol, UK.