Dear Jose,
> I used your script to produce an *.off file for amber. When I tried to
> produce the topology file, amber complained about missing CT-C-CT angle
> parameter. I found *CT-C-CT 63.0 117.0*
> in google, but I don't trust this much. Do you have this angle parameter in
> the acetone molecule?
You could use Antechamber to determine the missing force field
parameters (listed in a frcmod file) but only in association with the
General Amber Force Field. Or you can build this frcmod file by
yourself & provide the missing force field parameters for the force
field of your choice (amberXX, gaff, CHARMM, Glycam or OPLS): LEaP
will give you the list of missing force field parameters when you save
the prmtop/prmcrd files.
in $AMBERHOME/dat/leap/parm/ you will find templates for such a frcmod file.
Concerning missing bond/angle FF parameters, the best bet might be to
look in the parm99, gaff or glycam force field parameter files and
take them for there (they are not that important _if_ you are
interested in conformation & not in normal mode analysis). Concerning
missing dihedral FF parameters, this is another story: "Important"
dihedral should be refitted...
If you look in gaff, you will find:
c3-c -c3 62.8 116.05
As you can see your google search was correct ;-)
Either you decide to use gaff and you use it with Antechamber, or you
use amber99SB and you need to adapt it a little:
CT-C -CT YY XXX.X
My feeling is that 62.8 is too precise (I do not think such precision
is required): 60, 63 or 65 could be used, and XXX.X could come from
your own geometry optimization computation using a high basis set.
regards, Francois
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Received on Wed Sep 02 2009 - 23:04:58 PDT
