On May 27, 2011, at 6:17 PM, Jason Swails wrote:
> 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).
>
I can't speak to the eagerness to implement this, but I would speak against
promoting packmol for this. I've spent a lot of time learning all the ins
and outs of using packmol with AMBER. My bottom line is the two are a poor
fit. The inability to just take a system generated with packmol and LEaP and go
directly to equilibration without needing a lot of gyrations and hocus pocus is
my main reason for my speaking against packmol. There is a lot of (hard to
explain) black magic involved in successfully using packmol with AMBER. (For
the casual reader, see the archives of this list to read my and others' comments
about this point.) I would rather see either (1) an addition to LEaP as indicated
above, or (2, maybe better) an approach based on the utilities referenced in
Tutorial A13 (the XtalUtilities referenced there) promoted as the way to do this.
It should be possible, I believe, to use the XtalUtilities to achieve all the
important capabilities of packmol.
YMMV, but I do not think packmol is the cure all it would seem to be on casual
examination.
Bud Dodson
> 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
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Fri May 27 2011 - 17:30:02 PDT
