Hi,
I guess your findings below occur because nmode doesn't run properly.
Comment the lines
unlink $sanout;
unlink $sanres;
unlink $nmodeout;
in the funtion calc_NM in mm_pbsa.pl. You should now get the sander and
nmode output files in addition to the restart file after minimization by
sander. See if you can find anything wrong with them.
Best regards
Holger
> Dear Amber user,
>
> I am using nmode to study the entropy change of a ligand/protein complex. I
> used NM=1 for nmode calculation on mm_pbsa. It is OK for me to calculate the
> the ligand alone using
>
> _________________________
> COMPLEX 0
> RECEPTOR 0
> LIGAND 1
> ___________________________
>
> as input file for mm_pbsa.
>
> But, if I do the calculation for Recpetor by changing to
> _________________________
> COMPLEX 0
> RECEPTOR 1
> LIGAND 0
> __________________________
>
> or do entropy study for complex using
>
> ___________________________
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> __________________________
>
> I got a error message as following and I can't get any entropy value. All the
> number in the statistics.out file is 0.
>
> Use of uninitialized value at /amber7/src/mm_pbsa/mm_pbsa_statistics.pm line
> 1596.
> Use of uninitialized value at /amber7/src/mm_pbsa/mm_pbsa_statistics.pm line
> 1608.
> No skew or curtosis when zero variance in moment
> No skew or curtosis when zero variance in moment
>
> Any suggestion is welcome.
>
> Thanks,
> Wentao Fu
> Ctr. for Pharm. Biotech.
> University of Illinois at Chicago
> CHicago, IL 60607
--
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037 USA
phone: +1-858-784-9788
fax: +1-858-784-8896
email: gohlke.scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++
Received on Fri Apr 25 2003 - 23:53:01 PDT
