Re: [PyMOL] Can't figure out APBS

[Brian K. <bk...@it...>]

In addition to the stipulations listed below, I have also noticed 
that apbs can't handle a pdb file that has coordinate columns that 
touch each other such as this example:

				      this column
					V
ATOM     78  N   GLY A  38      66.914  66.219-103.497  1.00 18.01      A  
ATOM     79  CA  GLY A  38      66.309  66.763-104.698  1.00 20.04      A  
ATOM     80  C   GLY A  38      65.598  68.007-104.199  1.00 20.96      A  
ATOM     81  O   GLY A  38      64.432  68.267-104.508  1.00 23.61      A  

I've needed to transform the coordinates of my molecule so that this 
kind of thing doesn't happen.
(realspace_transform.inp in CNS works.)

Hope this helps.
BK

>Hi!
>
>You have to see if you are getting the .dx file. The default of  the 
>program is to put it at the same directory where it was installed, 
>along with the other temporary files: .in, .pqr and .pdb. In case of 
>not, I got the same problem and the solution was: the PDB that you 
>load can`t have chain ID, the aminoacids can`t have alternate 
>conformations and the program only accepts the standard residues. If 
>everything is all right with your PBD, after run the APBS you gotta 
>have the .dx at this directory. Once you got the .dx (the pymol will 
>show the apbs.map) click at the update (on Visualization) and then 
>show.
>Hope this help!
>sandra
>
>
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