AMBER Archive (2009)

Subject: Re: [AMBER] How to introduce the second protein molecule into simulation box?

From: Jason Swails (
Date: Fri Oct 16 2009 - 08:15:57 CDT

I think there may be an easier way... If you already have the PDB for the
monomer, then you can load it into leap and simply combine two of the pdbs
under a common name. The coordinates will place them right on top of one
another, but in xleap you should be able to drag one beside the other. This
is what I mean:

(in xleap)

source frcmod.ff99SB (or whatever FF you want to use)
monomer = loadpdb YOURPDB
aggregate = combine {monomer monomer}
edit aggregate (to bring up the aggregate in the xleap visualization window)
saveamberparm aggregate aggregate.prmtop aggregate.inpcrd

(don't forget to solvate if you want a solvated system). If you're having
trouble moving one molecule away from the other, try setting two monomers,
editing one and moving it away, and then combining those two.
monomer1 = loadpdb YOURPDB
monomer2 = loadpdb YOURPDB
edit monomer1 (and move it away)
aggregate = combine {monomer1 monomer2}

good luck!

On Fri, Oct 16, 2009 at 3:00 AM, Siddharth Rastogi <> wrote:

> Dear Amber users,I have x ray crystal structure for the monomer of a
> protein. This protein is well known for aggregation. I am interested to
> check aggregation tendency of this protein. so I want to start with two
> molecules of this protein. My question is how to introduce the second
> protein molecule into the simulation box?. I have in my mind to use chimera
> and open the same pdb file twice and then translate one model to certain
> distance and then write pdb for two models into a single file. And use this
> file in xleap to get top and crd files. Whether this is ok?. can any one
> help me in this regard.
> with regards and thanks,
> Siddharth Rastogi
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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