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.
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Feb 02 2011 - 14:30:03 PST
