On Thursday, May 12, 2011 at 9:03 AM"[email protected]" <[email protected]>
wrote:
> I am using GROMACS 4 to do MD simulations of protein-ligand complexes.I
> encountered some
> problems when generating the topology file of the ligands. I generate the
> topology file
> of ligands by using topolbuild package. The atom types of GAFF force field
> are assigned
> to the atoms of the ligand. However, when I used grompp command to write the
> tpr file.
> There is an error saying:
>
> Fatal error:
> Atomtype c3 not found
> For more information and tips for troubleshooting, please check the GROMACS
>
>
> It seemed that, the amber ff03 force field in gromacs 4 didn't include the
> atom types of
> the GAFF force field.
>
> Does any one have ever encountered the same problem? What can I do to solve
> this problem?
>
> It seemed that the atoms types in GAFF force field (e.g., c3, hx, hc,
etc. ) can not
> be recongnized by the amber ff03 FF implemented in
gromacs 4.5.3.
This is absolutely correct. GAFF atom types are not included in other amber
force fields.
However, for GAFF, the output of topolbuild includes an *nb.itp file that gives
the
atom types and the LJ parameters for those atom types. I've not tried mixing
amber
force fields like this, but I believe that if you include this up at the top
after including
your desired amber force field includes, everytihing should be defined
correctly.
I seem to recall others doing this already.
Sincerely,
--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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