Thanks. I have another question now.
I am preparing a mixture of two molecules in the ratio of 3:2.
I have the individual topology files of the molecules from tleap.
I have also generated the topology file for the mixture(3:2) from tleap
The number of dihedrals for the mixture is 685 (including impropers). The
individual number of dihedrals are 160 and 102 for each of the molecules.
Now for 3:2 ratio the total number of dihedrals should be 684 (3x160
+2x102). However I am getting one dihedral extra from the topology file of
the mixture.
Why is this so ?
Thanks
Arun
On Wed, Jun 24, 2015 at 1:19 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 24 2015 - 14:00:04 PDT
