On Wed, Sep 28, 2011, Neha Gandhi wrote:
>
> I have prepared a file using 20 peptides using packpol. I want the volume to
> be 1000 nm^3 to achieve a certain concentration. I am bit confused, how do I
> solvatebox using leap so that each side has 100 Ang.?
You can't. You could use packmol to create such a box, but even then, the
volume of the box will change once you do a constant pressure equilibration.
The only way I can think of to get a given peptide concentration is to
estimate how may waters you will need, then play with the "closeness"
parameter in solvateBox (or solvateOct) to get about that many waters.
Equilibrate the system and check the final volume. Add or subtract waters
if you have too small or too large a box. Repeat and rinse.
[You *could* use a molal scale for concentration, and then it is easy to
get a desired concentration, but that's probably not what you want....]
...good luck...dac
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Received on Wed Sep 28 2011 - 05:30:03 PDT
