AMBER Archive (2005)

Subject: Re: AMBER: how to make the prepin file for dimer and clusters of organic molecule in Amber7

From: David A. Case (case_at_scripps.edu)
Date: Fri Apr 15 2005 - 10:25:56 CDT

On Fri, Apr 15, 2005, Ananda Rama Krishnan Selvaraj wrote:

> i have made the prepin file for the organic
> molecule in amber7 and i am successful in the MD simulations of
> isolated molecule. now i have the problem in making the prepin
> file ,topology as well as coordinate files for more than one molecules
> like dimer and clusters. could anyone suggest the right path to make
> the input files for dimer and clusters of orgaic molecules for MD.

Make a PDB file with the intial coordinates you want, putting a "TER" card
between each monomer. Then use loadPdb in LEaP to read this in (after reading
in the prepin file you have for the monomer). The monomers should be
recognized, and the TER card will prevent LEaP from trying to make any
covalent bonds between monomers.

...good luck...dac

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