Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Feb 25, 2013 at 7:31 PM, Marek Maly <marek.maly.ujep.cz> wrote:
>
> > #3
> > Regarding substitution of PREPIN file by MOL2 file:
> >
> > There are some information in PREPIN file which
> > are not (at least by default) present in MOL2 like
> >
> > a)
> > IMPROPER record
> > which defines groups of atoms (using atom names) for which improper
> > torsions have to be used (e.g. aromatic rings).
> >
> > How to incorporate this important information into MOL2 file ?
> > I checked MOL2 format ( http://www.tripos.com/data/support/mol2.pdf )
> > and did not found any IMPROPER section.
> >
>
> This information should not need to be present --- tleap should
> automatically apply known improper torsions that it recognizes.
If it is added to a prep.in file (instead of a mol2) the list will
be checked against the impropers the FF assigns. This can be useful
for developing improper torsions. But for practical purposes the
list-improper-per-residue is superseded by the current FF.
> b)
> > In PREPIN file there is also section LOOP where all
> > the loops are defined but this info is sufficiently
> > substituted in MOL2 file by the complete list of all
> > bonds I guess. Am I right ?
>
> I don't know what the LOOP section does.
It closes loops that wouldn't otherwise be closed with the stack-based
algorithm used by the old PREP program and emulated by leap for reading
prep.in files. Correct: a complete bond list accomplishes the same thing.
> c)
> > There are also 3 DU atoms in the start
> > of the atom list in PREPIN file defining
> > cartesian system. Are these DU atoms
> > necessary also in case of MOL2 definition
> > of the given residuum /molecule? If yes how to define
> > them ?
> >
>
> DU atoms are only necessary because the PREPIN uses internal coordinates
Prepin can handle cartesian too - XYZ keyword I believe. Maybe DU's
are expected there too.
Bill
> (that is the IN part of prepin -- prepc or prepcar files use cartesian
> coordinates). The dummy atoms are necessary to uniquely define the
> position of the first, second, and third atoms. [2]
>
>
> Ultimately, there is only one thing that the prepin file has that the mol2
> file does not --- connection information. The prepin file allows you to
> specify a head and tail atom so that tleap will automatically chain it to
> adjacent residues. You can set those atoms by hand, though, and the q4md
> folks modified the mol2 file to add this data (see the mol3 documentation
> on their website, which is supported in AmberTools 12).
>
> References:
> [1]: <hearsay>It had some clever code that was able to efficiently
> calculate TIs by only calculating the pairwise differences. However, it
> was not well-parallelized, and when pairwise-decomposable methods (cutoffs,
> distance-dependent dielectric) began to be replaced by non-pairwise
> decomposable methods (Ewald, GB, PB), this approach was no longer
> rigorously correct. Therefore, TI was implemented using a dual-topology
> approach in sander and Gibbs was dropped. </hearsay>
>
> [2] I suspect this is really just an implementation detail. Since the
> positions of DU are arbitrary, so is the position of the first 3 atoms,
> technically---at least in Cartesian space. Adding 3 dummy atoms does allow
> the first atom's position to be specified by a distance, angle, and
> dihedral, just like every other atom.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 25 2013 - 18:00:02 PST
