RE: [Apbs-users] Re: your mail

[Nathan B. <ba...@bi...>]

Hi Frank --

Have you run these PQR files through psize.py in APBS?  What grid sizes does
it recommend?  If you *must* use a smaller grid, you should switch BCFL from
"sdh" to "mdh".  This will slow the calculation down but will give you more
accurate potentials/energies.

-- Nathan

--
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone:  (314) 362-2040, Fax:  (314) 362-0234
URL:  http://www.biochem.wustl.edu/~baker  

> -----Original Message-----
> From: Frank D. Ducheneaux [mailto:fr...@wa...] 
> Sent: Thursday, October 14, 2004 3:29 PM
> To: Nathan Baker
> Cc: 'APBS'
> Subject: RE: [Apbs-users] Re: your mail
> 
> Nathan,
> 
> srfm = smol
> bcfl = sdh
> 
> I am guessing that calcualtion done at glen = 70 changed from 
> the previous calculation because the length was just not long 
> enough.  Especially since the one at glen = 53 failed because 
> atoms were found outside of the grid.  
> I tried to send the .pqr files but it was too large and the 
> moderator would not put the email thru.  I can post them to 
> my web site if you would like to see them. 
> 
> 
> On Wed, 13 Oct 2004, Nathan Baker wrote:
> 
> > Hi Frank --
> > 
> > This sensitivity on GLEN is very disturbing.  What were 
> your SRFM and 
> > BCFL settings?
> > 
> > Thanks,
> > 
> > Nathan
> > 
> > 
> > --
> > Nathan A. Baker, Assistant Professor
> > Washington University in St. Louis School of Medicine Dept. of 
> > Biochemistry and Molecular Biophysics Center for 
> Computational Biology 
> > 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
> > Phone:  (314) 362-2040, Fax:  (314) 362-0234
> > URL:  http://www.biochem.wustl.edu/~baker
> > 
> > > -----Original Message-----
> > > From: apb...@ch... 
> > > [mailto:apb...@ch...] On Behalf Of Frank D. 
> > > Ducheneaux
> > > Sent: Tuesday, October 12, 2004 10:55 PM
> > > To: APBS
> > > Subject: [Apbs-users] Re: your mail
> > > 
> > > > 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 127-72
> > > Pasadena, CA 91125
> > > (626)395-2689
> > > 
> > 
> > 
> 
> --
> Frank Ducheneaux
> Caltech
> Division of Chemistry
> m/c 127-72
> Pasadena, CA 91125
> (626)395-2689
>