On Mon, Jul 23, 2012, aneesh cna wrote:
>
> I am working with MD simulation of DNA systems. I was trying to generate
> topology (*.top) file for some selected atoms of the DNA ( few nitrogen and
> oxygen of some bases in DNA )that are not connected to each other.
Topology files describe real molecules, and allow their energies to be
estimated as a function of conformation. LEaP is not intended to create
topology files for just a few selected atoms.
> Whenever
> I try to run the leap with a pdb file containing (only) these atoms ( TER
> card inserted), leap automatically add all the other missing atoms.
Exactly. It's not clear why you want to make the topology file (i.e. what you
would do with it). It might be that the parmed program could help you out,
but be careful, since none of our tools were designed to do the sort of thing
you describe.
...dac
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Received on Mon Jul 23 2012 - 06:30:03 PDT
