> Hi all,
>
> I am having some difficulty understanding the results that I am getting
> for a series of calculations that I have performed on carboxypeptidase V.
> I did four calculations on this molecule varying only the glen and dime
> parameters (grids spacing, of course, varied slightly around 0.55).
>
> I first used the psize.py script to determine the longest axis of the
> molecule to ensure that the molecule fit within the box. I chose glen of
> 105, 90, 70 , and 53 in the x,y,z directions for the four calculations.
> The results of the psize.py were:
>
> ################# MOLECULE INFO ####################
> Number of ATOM entries = 4791
> Number of HETATM entries (ignored) = 0
> Total charge = 2.000 e
> Dimensions = 9.995 x 46.641 x 45.355 A
> Center = 5.000 x 19.395 x 8.950 A
> Lower corner = 0.002 x 3.926 x 31.627 A
> Upper corner = 9.997 x 42.715 x 13.728 A
>
> .............................
>
> The polar free energy of solvation for each glen was 6230, 6210, 5289
> for glen = 105, 90, and 70, respectively. However, the calcualtion for
> glen = 53 failed because some of the atoms fell outside of the box.
> Perhaps I am missing something crucial since the psize.py molecular
> dimensions gave the longest axis less than the glen and I figured this
> would allow the box to fully encompass the system. Also, I noticed that
> the glen = 70 energy was much greater than the previous claculations using
> larger glen so I assume I allowed the box edges to come too close the
> molecular extremes. Again, this alarmed me and I am afraid I am using the
> psize script or APBS grid settings incorrectly. Any ideas? I ahve
> attached the original .bgf file which was converted into the usable
> .pqr file, also attached. Thanks in advance.
>
>

Frank Ducheneaux
Caltech
Division of Chemistry
m/c 12772
Pasadena, CA 91125
(626)3952689
