On Sat, Apr 16, 2011, hanlu0366 wrote:
>
> I am a graduate,a novice simulating
> molecular crystals dy Amber
> so I want to inquire you how to
> construct a .prepi of a super cell 2*3*1 about the crystal of DT-TTF
I think you are somewhat confused here, or perhaps I don't understand your
question. You would generally create a "prepi" (or "mol2") file of an
individual TTF molecule. The antechamber program will give you a trial set of
parameters, which you might use as is, or tweak by hand.
Then, you would have to construct a pdb file the unit cell. Amber has a
UnitCell program that helps with this (see tutorial A13), but it's input
format is pdb, not cif. (You might look for programs to convert cif to pdb
format.)
Then you need to construct the supercell, which must be at least 20 Ang. on a
side (and hence probably bigger than you cite above). The PropPDB program can
probably help with this.
I'm not aware of people using Amber to carry out crystal simulations of such
small molecules, so you may have to experiment some.
> At first , I try to construct a
> .prepi of super cell about a molecular crystal from a .prepi of a
> monoer. but in next step ,when I had get the .prepi of supercell ,I
> found that there is only coordinates of monomer in .prepi of super
> cell.
If you do have problems, and want help, emails like the above are not much
help: you are describing what you *intended* to do ("construct a .prepi of a
supercell") but not what you actually did (the programs you ran, the exact
comands you gave, and the specific problems with the output.)
....regards...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 16 2011 - 06:30:03 PDT
