Re: [AMBER] How to get the prmtop and inpcrd files of melamine in Amber?

From: David A Case <>
Date: Fri, 6 Sep 2013 08:31:05 -0400

On Fri, Sep 06, 2013, 张明焜 wrote:

> I am a amber beginer,I know the prmtop and inpcrd files of a protein can be
> produced by a ready PDB file ,but how can I get the prmtop and inpcrd files
> of a small molecule like melamine(H2N-CH2-COOH) which has not a ready PDB
> file ?

If you have coordinates in some format, you would need to convert it to PDB
format. If you don't have any coordinates, you can use programs like ChemDraw
or xleap to draw the molecule on the screen and create coordinates.

Once you have a set of coordinates, you will need to use antechamber to
generate a force field: see Tutorial B4 for an example.

Finally, melamine is C3H6N6, and is nothing like the molecule you describe
above. What you wrote is a gas-phase version of glycine.


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Received on Fri Sep 06 2013 - 06:00:03 PDT
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