On Wed, Jun 24, 2015 at 1:07 PM, Arun Srikanth <askforarun.gmail.com> wrote:
> Hello Amber users.
>
> I have a general question regarding generating topology file using
> antechamber.
>
>
> Let's say I have a mol2 file. I load the mol2 file in leap and generate
> topology file after checking the unit using the command
>
> check SUS
> The result is
> Checking 'sus'....
> Checking parameters for unit 'sus'.
> Checking for bond parameters.
> Checking for angle parameters.
> Unit is OK.
>
>
> Now I have not loaded the frcmod file for this molecule since the leap said
> the unit is ok and there were no missing parameters.
>
>
> However I load the frcmod file (as given below)
> remark goes here
> MASS
>
> BOND
>
> ANGLE
>
> DIHE
>
> IMPROPER
> ca-ca-ca-ha 1.1 180.0 2.0 General
> improper torsional angle (2 general atom types)
> ca-ca-ca-os 1.1 180.0 2.0 Using default
> value
> c3-n -c -o 10.5 180.0 2.0 General
> improper torsional angle (2 general atom types)
>
> NONBON
>
> And now I generate the topology file.
>
> The topology generated before and after using the frcmod file is not the
> same i.e the number of dihedrals is not the same.
>
> Should I be concerned ?
>
Maybe. (Therefore, yes).
> Which topology is correct
>
The one after you load the frcmod file is typically better. The only
difference between using and not using your frcmod file is the definition
of three improper torsions. These parameters are the most difficult to
assign in general (every program may do them slightly differently), since
there is no well-defined order of the atoms (there is one central atom that
is bonded to the other 3 usually, so only the placement of that central
atom is well-defined in the definition of an improper torsion). And the
improper torsions are typically only needed to maintain planarity of a
conjugated system if the existing parameters don't do a good enough job of
that.
As a result, tleap will try to find centers where you might expect to find
improper torsions, then try to see if there are any improper torsions
*defined* for that center. If not, it assumes the existing parameters do a
good enough job and moves on. If an improper torsion is defined, it goes
ahead and adds that improper torsion to the list of dihedrals.
So in your example, the improper torsions for the aromatic, conjugated
system (and the c3-n-c-o group, which looks like an amide bond, perhaps)
are only applied if you generate the topology after you load the frcmod
file. Those atom types seem to me like they should exist in a group of 4
atoms that are typically planar, so it's most likely better to have those
improper torsions defined in your prmtop.
Note that for every other type of parameter -- like bonds, angles, and
proper dihedrals -- this issue doesn't exist. The terms *must* exist or
tleap complains about missing parameters.
HTH,
Jason
>
> Arun
>
>
>
> Thanks
> Arun
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jun 24 2015 - 10:30:03 PDT
