Hi, David and Jason:
Thanks a lot for the answering. I use the amber14 which is just
installed last month. The probem is that the tleap can load the structure
successfully, and also can build a prmtop file and inpcrd file without an
error. But the inpcrd is missing 78 atoms.
And also, when we build the pdb, it contains the right number of
atoms. And the pdb file can be loaded into the prmtop file in VMD. We know
the prmtop and pdb file have the same number of atoms. Do you have any idea
why tleap build an incomplete inpcrd file?
Thanks a lot!
Li
On Mon, Jul 28, 2014 at 6:36 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Sun, Jul 27, 2014 at 4:06 PM, 肖立 <xiaoli19871216.gmail.com> wrote:
>
> > Hello:
> > I use the amber14 tleap to generate an inpcrd file. I shows the
> > following message:
> > "
> > Checking Unit.
> > WARNING: There is a bond of 0.284304 angstroms between:
> > ------- .R<NAP 262>.A<C1B 12> and .R<NAP 262>.A<N9A 13>
> > WARNING: There is a bond of 0.255071 angstroms between:
> > ------- .R<NAP 520>.A<C1B 12> and .R<NAP 520>.A<N9A 13>
> > WARNING: The unperturbed charge of the unit: -0.993997 is not zero.
> >
> > -- ignoring the warnings.
> >
> > Building topology.
> > Building atom parameters.
> > Building bond parameters.
> > Building angle parameters.
> > Building proper torsion parameters.
> > Building improper torsion parameters.
> > total 1492 improper torsions applied
> > Building H-Bond parameters.
> > Incorporating Non-Bonded adjustments.
> > Not Marking per-residue atom chain types.
> > Marking per-residue atom chain types.
> > (Residues lacking connect0/connect1 -
> > these don't have chain types marked:
> >
> > res total affected
> >
> > CTYR 2
> > NAP 2
> > NSER 2
> > OCT 1
> > WAT 11317
> > )
> > (no restraints)
> > "
> > The inpcrd file is not generated right. It misses several coordinate
> > information as well as the box information.
>
>
> > I'm wondering if anyone can tells me why?
> >
>
> This sounds like the bug fixed by update.2 for AmberTools 14 -- see
> http://ambermd.org/bugfixesat.html. Specifically the description for the
> tleap fixes:
>
> tleap:
> Fixed occasional inpcrd file truncation
>
> Please make sure that you have applied all updates to AmberTools. If you
> reconfigure and recompile Amber, it will ask you if you want to update your
> source code (and recompiling will make those changes take effect).
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com
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Received on Mon Jul 28 2014 - 16:30:02 PDT
