Thanks Jason and Dmitry for your suggestions.
On Thu, Feb 3, 2011 at 11:39 AM, Dmitry Nilov <nilovdm.gmail.com> wrote:
> The choice of the force field actually depends on your task. ff99SB is
> very effective for protein simulations that was approved in a number
> of articles.
>
> On Thu, Feb 3, 2011 at 6:47 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> wrote:
> > Hi Jason,
> > As you mentioned about the force field, I have a query regarding the
> same.
> > How can I enlist all available force fields in my installed Amber10
> version.
> > And for modeled protein (containing a long loop region predicted by
> > ab-initio calculations), which forcefield would be better to proceed
> > further.
> >
> > Hirdesh
> > On Thu, Feb 3, 2011 at 3:37 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
> >
> >> If you don't load a force field (i.e. source leaprc.ff99SB), then as
> soon
> >> as
> >> you load the PDB you're hit with similar messages. However, Bill is
> right:
> >> the FATAL messages will only appear after a failed "saveamberparm',
> which
> >> means that *some* force field parameters were loaded. However, these
> lines
> >> (along with many others) are worrisome
> >>
> >> FATAL: Atom .R<CYS 2510>.A<C 3> does not have a type.
> >> FATAL: Atom .R<CYS 2510>.A<O 4> does not have a type.
> >>
> >> CYS is a standard residue in every force field, and C and O are standard
> >> atomic names in the current and previous recent PDB standards. As such,
> I
> >> have to conclude that no *correct* force field was loaded. Perhaps the
> >> user
> >> initially just loaded their frcmod that they created for a custom
> residue
> >> but not any full force field (i.e. leaprc.ff99SB). I think this
> reproduces
> >> that error.
> >>
> >> It could also be a case of corrupted template files, I'm really not
> sure.
> >> Not quite enough information was given to debug this issue.
> >>
> >> All the best,
> >> Jason
> >>
> >> On Wed, Feb 2, 2011 at 3:24 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>
> >> > That would have the symptom of missing parameters, not missing types.
> >> >
> >> > > or, as Jason said, in inappropriate force field selected (or not
> >> > > selected at all)..
> >> > >
> >> > > On Wed, Feb 2, 2011 at 10:59 PM, Dmitry Nilov <nilovdm.gmail.com>
> >> wrote:
> >> > > > It seems that your problem results from incorrect atom names in
> input
> >> > > > pdb (is it pdb?) file.
> >> >
> >> >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Graduate Student
> >> 352-392-4032
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Dmitry Nilov,
> Faculty of Bioengineering and Bioinformatics,
> Lomonosov Moscow State University
>
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>
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Received on Thu Feb 03 2011 - 01:00:02 PST
