On Thu, May 26, 2011 at 3:06 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > If you need them to have the same number of waters, you can tinker
> > with the buffer size of the smaller system until you get the right
> > number.
>
> It seems people want to set the number of waters often enough that
> it might be worth adding to leap. The simplest approach I can think
> of would be a new cmd that would reduce the number of waters by
> random subtraction to a specified amount.
>
Eh, I don't know how great of an approach this is. I think what people
would want the most is to be able to specify a certain number of water
molecules and have LEaP set the box around it appropriately. There should
only be 1 independent variable b/w box size and number of waters, so to make
users specify both is a risky combo. Better to let dedicated software
packages intended to deal with this actually do this (e.g. packmol), or add
the whole new functionality to do it 'properly' in LEaP (I think we'd be
hard-pressed to find someone eager to do this).
In any case, 'random' subtraction is doable in a 2-step process using a
leap- or ptraj-generated PDB file as an intermediate (and then reading that
back through leap after you remove a couple waters).
All the best,
Jason
> Bill
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri May 27 2011 - 16:30:03 PDT
