Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Apr 23, 2013 at 2:47 PM, Jonathan Gough
> <jonathan.d.gough.gmail.com>wrote:
>
> > I have a pdb (from an x-ray structure) that was missing several
> > "loops"(they are floppy therefore were very disordered in the crystals).
> > I used swisspdb viewer to add the residues back in but on a few of the
> > "connections" it was a stretch.
> >
> > therefore leap warns me that
> >
> > WARNING: There is a bond of 6.802961 angstroms between:
> > ------- .R<SER 363>.A<C 10> and .R<ARG 364>.A<N 1>
> > WARNING: There is a bond of 3.723094 angstroms between:
> > ------- .R<SER 990>.A<C 10> and .R<ARG 991>.A<N 1>
> > WARNING: There is a bond of 4.437505 angstroms between:
> > ------- .R<ALA 1197>.A<C 9> and .R<VAL 1198>.A<N 1>
A situation like this begs for inspection in xleap, which has the
useful ability to select and minimize groups of atoms (using basic
rules and without the vdw term). The slightest knowledge of chemistry
will often result in something that will minimize nicely in sander or
pmemd.
Note this is the only place leap's idea of bond order might matter -
adjust by double-clicking on bonds if so.
That said, low temperature dynamics will solve a lot of problems, and
give an interesting movie no matter what.
Bill
> >
> > and (of course?) there aren't any improper torsion parameters and I get
> > more warnings.
> >
> > the question is
> >
> > 1 - can I still use what I have and minimize (I think I have tried this
> > several different ways and things go crazy)? If so any suggestions on how
> > to go about doing it? (I tried/thought I could do it in implicit and
> > explicit solvent followed by slow heating with heavy constraints and short
> > times steps.)
> >
>
> What happens if you use strong positional restraints (~500-1000 kcal/mol)
> on the part of the structure that started out OK and then minimize only
> those residues that had to be 'built-in'? For such a strained structure,
> you should set ncyc to a very large number to make sure that
> steepest-descent minimization is used instead of switching to the conjugate
> gradient minimizer after 10 steps or so.
>
> An alternative is to set temp0 to 0 K and run dynamics instead of
> minimization, using a very short time step (e.g., 0.0001 or maybe even
> lower -- try experimenting here), but I would suggest trying the
> minimization first.
>
> I would do this all in implicit solvent, too, to avoid wasting time dealing
> with the explicit solvent molecules. Then you can create a PDB based on
> this structure and solvate if necessary.
>
> Alternatively, does SwissPDB viewer have a minimization option that may be
> able to relax the structure?
>
>
> > 2 - is there a "trick" to fixing what I have?
> >
>
> There are lots of tricks. I would start with setting ncyc to a large value
> and setting strong restraints on the 'known' coordinates, allowing only
> those that swissPDB viewer added to relax.
>
>
> >
> >
> >
> > 3 - is there a better (easier) way to build out missing residues denovo
> >
> > (letting amber build them by leaving out the residues does not work as it
> >
> > fills in the missing atoms in a straight line - not in a loop as I need)
> >
>
> The archives of this mailing list may have some useful tidbits (I recall
> this type of thing being discussed before, but can't remember specifics).
> I'm sure there are better alternatives, but I have no experience with them.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Apr 23 2013 - 21:30:02 PDT
