Check _MMPBSA_complex.mdcrd, _MMPBSA_receptor.mdcrd, and
_MMPBSA_ligand.mdcrd with your corresponding topology files (visualize
them). I'm guessing based on the error messages given, your structures will
probably look warped.
The solution is to make sure that strip_mask is properly set and that your
topology files are consistent with each other.
Hope this helps,
Jason
On Mon, Aug 1, 2011 at 5:00 PM, Irene Newhouse <einew.hotmail.com> wrote:
>
> I'm getting the following error when I try to do MMGBSA on a trjaectory:
>
> Preparing trajectories with ptraj...
> checkCoordinates(): Could not predict number of frames for AMBER trajectory
> file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> checkCoordinates(): Could not predict number of frames for AMBER trajectory
> file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> checkCoordinates(): Could not predict number of frames for AMBER trajectory
> file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
> 250 frames were read in and processed by ptraj for use in calculation.
>
> The original trajectory is a NAMD dcd file, and that hasn't been an issue
> to date, but just to be sure, I used ptraj to convert a 250 -frame selection
> from the total dcd file to mdcrd format & tried again. Same thing.
>
> Does anyone have any advice for me?
>
> Irene Newhouse
>
>
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Aug 01 2011 - 18:00:03 PDT
