[gmx-users] Definition of mol2 file used by topolbuild

Bruce Ray brucedray at yahoo.com
Tue Mar 18 19:47:59 CET 2008

Apparently, my documentation for topolbuild is not
sufficiently precise in the definition of the input
molecular structure file.

The program, topolbuild, is described as taking a mol2
file as input.  By mol2 file, I mean a syntactically
correct mol2 file with Tripos atom types and charges,
and with all hydrogens present such as Sybyl would
write, and not merely a file that has the general
format of a mol2 file.  While topolbuild can generate
a gromacs topology with other atom types, such as gaff
or amber, these will not work in the input simply
because such types would not be written by Sybyl.

Chimera from UCSF will write a file that meets this
specification.  Antechamber can be instructed to write
a file that meets this specification if one sets it
for tripos atom types and gas charges.  I presume that
there are other programs that can write a file that
meets this input specification.  However, I would
advise anyone who uses a program other than Sybyl to
generate a mol2 file for topolbuild input, check the
mol2 file so produced to be sure that all atom types
and all bond types are correct for the molecule you
desired, and that all hydrogens in the molecule are
present.  On occassion, I have seen output from
conversion of pdb files to mol2 files that has had
single bonds where double or aromatic bonds should
have been, and that has had sp3 carbon types where
sp2 types should have been.

Please also be aware that the topology generated by
topolbuild needs to be checked as well.  A particular
item to check would be parameters for the dihedral
angles because some of the tables from antechamber
used to set the topology parameters do not include
every possible combination of atom types in the
dihedral angle parameters.  In addition, please note
that the non-bonded itp file written by topolbuild
includes any ions that were present in the mol2 file.
Typically, parameters for these ions would be found
in ions_gaff.itp and ffusernb.itp that are included
with topolbuild in the water_and_ions subdirectory.
Thus, the duplication of these in the non-bonded itp
file written by topolbuild needs to be deleted to
avoid an error message about the duplicate entries
from grompp.

I hope that this clarifies the meaning of mol2 file
and saves future users from experiencing these
particular problems with the program.


Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273

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