[gmx-users] AMBER to GROMACS conversion
Bruce D. Ray
brucedray at yahoo.com
Wed Jun 26 14:07:55 CEST 2013
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.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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