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

From: Jason Swails <>
Date: Fri, 6 Sep 2013 07:58:06 -0400

On Thu, Sep 5, 2013 at 11:52 PM, 张明焜 <> wrote:

> Dear professor :
> 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 ?

Generate a PDB file somehow. There are many ways. You can use a drawing
program (e.g., ghemical, Avogadro, Accelrys's DS Visualizer, ​​gabedit,
xleap if you like). To avoid drawing each atom by hand, you can typically
use a SMILES string (like c1(nc(nc(n1)N)N)N for melamine:

Note, 'one program' will rarely be sufficient to carry out every step of
your workflow. For instance in this case you know that you can get your
prmtop from a PDB file, so you can reduce the challenge here to figuring
out how to generate a PDB file. And don't limit yourself to looking at
utilities that Amber provides to do everything. And feel free to
experiment if you're unsure. That's often the best way to learn and
certainly helps provide a deeper understanding of the underlying programs
and methods.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 06 2013 - 05:00:02 PDT
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