Hello,
There are two common causes for this error. The most common is that
the prmtops and trajectory files are incompatible. The script should
save trajectory files for the complex, receptor, and ligand since the
script failed (named _MMPBSA_receptor.mdcrd, _MMPBSA_complex.mdcrd,
and _MMPBSA_ligand.mdcrd). You should visualize these trajectory
files along with your prmtop files to make sure that they're
compatible.
Incompatible trajectory/prmtop files can also be caused by incorrectly
setting receptor_mask and ligand_mask, so you should make sure these
are correctly set as well.
Good luck!
Jason
On Mon, Jan 4, 2010 at 3:56 AM, xueqin pang <pangxueqintea.yahoo.com.cn> wrote:
> Hello every,
>
> I am trying to calculate binding free energy of a protein/ligand system using mm-pbsa.py. And get the error: Sander output is missing values! VDWAALS=**********
>
> I have tried to change my input prmtops still get the same error
>
> does anyone have this problem and any suggestion is greatly welcomed
>
> thanks
>
> Pang Xueqin
>
> DICP CAS
>
>
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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 Mon Jan 04 2010 - 05:00:03 PST
