[gmx-users] AMBER to GROMACS conversion

[Bruce D. Ray]

On Tuesday, June 25, 2013 8:10 PM, Parker de Waal <Parker.deWaal09 at kzoo.edu> wrote:


> Now I've been able to successfully convert the two .mol2 files into gromacs
> .itp however I am unsure how to convert the .frcmod file as well.

 
I'm sorry, but while topolbuild does convert *.mol2 files into gromacs *.itp files
with AMBER parameters, it does not make use of AMBER files.  Therefore,
topolbuild 1.3 will not convert the *.frcmod files.

You should edit your *.itp file with any text editor to change entries according
to what is found in the desired *.frcmod file.  I should also note that the output
from topolbuild 1.3 requires some text editing to be made compatible with
GROMACS versions greater than 4.0.* because the arrangement of parameter
files within the GROMACS */share/gromacs/top directory was changed and
topolbuild has not been updated for that change.  Finally, I need to note that
for AMBER forcefields in GROMACS naming of atom types was updated to
be the standard AMBER atom type names with release of the GROMACS
4.5.* series, but topolbuild 1.3 does not reflect that change either.



-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273