Re: [AMBER] cReAtInG PDB

From: David A Case <david.case.rutgers.edu>
Date: Thu, 11 Apr 2019 10:06:11 -0400

On Thu, Apr 11, 2019, Bouthe´na 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


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Received on Thu Apr 11 2019 - 07:30:03 PDT
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