wentaofu wrote:
>
> Dear Amber users:
>
> I tried a mm_pbsa calculation on a Protein/Ligand complex and get the
> following results. The PBCAL is 0. I checked my input and I used the same
> parameters as the examples gaven by amber. Would you please give me some
> suggestions on how this can happen?
Hi,
check if you use the proper delphi version - we used the "academic"
version of delphi II for mm_pbsa. You might also want to comment the
"unlink $delphiout;" line in the calc_PB function in mm_pbsa.pl. This
will give you the delphi output file, which contains information of what
might have gone wrong during the calculation.
Best regards
Holger
>
> Thanks,
> Wentao Fu
> Ctr. for Pharm. Biotech.
> University of Illinois at Chicago
>
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -153.60 9.38
> VDW -42.24 3.32
> INT 0.00 0.00
> GAS -195.84 9.94
> PBSUR -2.85 0.19
> PBCAL 0.00 0.00
> PBSOL -2.85 0.19
> PBELE -153.60 9.38
> PBTOT -198.69 10.01
> GBSUR -3.66 0.25
> GB 152.13 8.29
> GBSOL 148.47 8.21
> GBELE -1.48 4.50
> GBTOT -47.37 4.08
--
+++++++++++++++++++++++++++++++++++++++++++++
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 May 16 2003 - 22:53:01 PDT
