Hi,
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?
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??
Please Suggest!
Thanks and regards,
Jac
On Mon, Apr 13, 2015 at 8:20 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Mon, Apr 13, 2015, jacob wick wrote:
> >
> > I have a crystal structure of an organic molecule from crystallographic
> > database. I want to see how the molecule will look like in packed state
> > (arrangement of the molecules in 3-D) i.e. when it is not alone but in
> the
> > presence of many such molecules in the solid packed state.
>
> Standard visualizaion programs like Chimera, VMD, etc will do this, as will
> the Mercury program from CCSD (if that is the database you are using).
>
> In Amber, you would use the UnitCell command (to create a single unit
> cell),
> and the PropPdb command to create adjacent unit cell.s
>
> ....dac
>
>
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Received on Tue Apr 21 2015 - 01:30:02 PDT
