On Thu, Apr 11, 2019, Boutheïna KERKENI wrote:
>
>I have 200 water molecules forming a Layer, and one organic molecule
>propylene that is on top of this layer. I hvae the XYZ coordinates.
>
>1) Please would you give a hint on how to creatae the PDB, to be able
>to create PRMTOP an INPCRD, certainly I need to provide framed for the
>propylene.
The answer depends on what file format the XYZ coordinates are in. But
the openBabel program (along with many other tools) will convert lots of
formats into PDB-format.
>
>2) I need to minimise and do MD by fixing the LAYER, can I perform NON
>periodic calculations (ntb=0)?
I don't see why not...give it a try, and see if you are satisfied with
the results.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 11 2019 - 07:30:03 PDT
