> I am dealing with a very large structure (a protein polimeric complex) and I
> mast add, in order to neutralise the system, more than 2000 sodium ions. The
> addions command in leap calculates an electrostatic grid to place the ions,
> but this calculation is very time consuming. Actually I think that a random
> positioning of the ions around the protein would be ok anyway. Is it
> possible to make leap to add ions randomly?
> Looking at the manual I couldn't manage to find options to do that or to
> modify the grid spacing of the electrostatic calculation or other parameters
> to speed up the calculation.
There used to be a way to set the grid spacing, but I forget what
it is; it might be an option of the 'set' command, and it may be
necessary to read code to find it if not covered in the manual.
Random placement sounds like a great option to have; if waters
are present, the ideal would be to replace them at random (there
would be no need to generate random coordinates). One way you
might approximate this is to replace every Nth water in a pdb
with an ion using some sort of shell script, then loadpdb and
setbox.
Bill
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Received on Thu Oct 07 2010 - 10:00:04 PDT
