In this case, they are all the same molecule and so the ordering becomes
irrelevant. A molecule is a closed set of atoms, in the sense that every
atom within a 'molecule' can be reached by every other atom in that
'molecule' *only* by traversing covalent bonds. If there is no pathway,
they must be in different molecules. Since each metal is bound to each
chain, both chains and metals are contained in the same set.
HTH,
Jason
On Mon, Jul 2, 2012 at 4:23 PM, Dhruva Chakravorty <dkchaks1.gmail.com>wrote:
> Hello,
>
> Just so we are all clear on this, what is the correct sequence when both
> metals bind o both chains, i.e. metal1 and metal2 bind to both chains 1 and
> 2 as well ?
>
> With regards
>
> Dhruv
>
> On Jul 2, 2012, at 3:58 PM, David A Case wrote:
>
> > On Mon, Jul 02, 2012, Ilyas Yildirim wrote:
> >
> >> Assume that you have a protein-DNA system. And assume that you define
> >> two heavy atom such as AU or AG which are covalently connected to some
> >> of the residues in protein.
> >>
> >> Assume that one does not include these heavy atoms in a mutated residue
> >> but explicitly use the 'connect' command in leap to create the covalent
> >> bonds. If the 'frcmod' includes all the necessary parameters, leap will
> >> create prmtop and inpcrd files without any issues. Savepdb command will
> >> also create the rigth sequencing of the system (let's say it is called
> >> mol.pdb).
> >>
> >> Now, if I use 'ambpdb -p prmtop <inpcrd> inpcrd.pdb', the file created
> >> is not right (not similar to mol.pdb). This was discussed before (in
> >> 2005) and the main issue wass because of the way ATOMS_PER_MOLECULE is
> >> defined in the prmtop file. I can understand that because the AG or AU
> >> atoms which are connected to proteins explicitly will be included in
> >> the proteins and they will not be seen
> >
> > There is an (unstated, I think) restriction on how cross-links can be
> added
> > in LEaP: the atoms involved in the resulting molecule(s) must be
> contiguous
> > in the Amber atom sequence. Thus, the following should work:
> >
> > chain1
> > metal1
> > chain2
> > metal1
> >
> > followed by the formation of a bond between chain1 and metal2, and/or
> between
> > chain2 and metal2. The the following would not work:
> >
> > chain1
> > chain2
> > metal1
> > metal2
> >
> > Now, if you make a link between metal1 and chain1, you get a new molecule
> > (made up of the atoms in chain1 plus metal1) that are not contiguous
> > in atom sequence. In this case, LEaP doesn't complain, but creates an
> > incorrect prmtop file (with a bad ATOMS_PER_MOLECULE section.) The
> > ambpdb program uses this information to create (bad) TER cards; but
> > the sander/pmemd programs also use this (bad) information in computing
> > pressures. So, the prmtop file has to be fixed.
> >
> > Some notes:
> >
> > 1. As Jason points out, the parmed program can diagnose and attempt to
> fix
> > this; for the second example above, I'm assuming it would bail out, since
> > there is no proper fix without completely re-ordering all the molecules.
> >
> > 2. There are other programs that do sanity checks on prmtop files: we
> need
> > to assemble these into a single place, ideally something that could be
> > automatically run when a prmtop file is created in the first place.
> >
> > 3. LEaP should at a minimum refuse to accept an order for which the
> > ATOMS_PER_MOLECULE section would be wrong. It could also reorder things
> > to make them correct, although that reordering might not be the one the
> > user really wants.
> >
> > 4. The analysis above may be wrong or incomplete: there may be times
> when LEaP
> > creates bad ATOM_PER_MOLECULE records that cannot be explained by the
> > reasoning above. If you have such a case, please post an example.
> >
> > ...dac
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Mon Jul 02 2012 - 13:30:03 PDT
