On Tue, Apr 21, 2015, jacob wick wrote:
> As suggested, I tried to reproduce the below tutorial:
> *http://ambermd.org/tutorials/advanced/tutorial13/Construction.html
> <http://ambermd.org/tutorials/advanced/tutorial13/Construction.html>*
>
> I am wondering that is this protocol is valid for constructing a lattice of
> small molecules like salicylic acid or it is ok for bio-molecules only?
This is fine for any size molecule. We often use these tools to prepare
crystal simulations of small molecules.
>
> what if I have a novel molecule whose structure detail is not present
> anywhere, i.e. sketched using chemdraw and then saved as pdb file??
Sounds like you are trying to *predict* a crystal form. That is beyond the
capabilities of Amber (for most molecules). To use the tools in tutorial A13,
you need to know the space group and the lattice parameters, which it sounds
like you don't have. You might look at some literature on prediction of
structures for organic crystals, but that is a very difficult and in general
unsolved problem. You might want to try it, but it's a research problem, not
something you just do by following a tutorial.
...good luck...dac
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Received on Wed Apr 22 2015 - 08:30:04 PDT
