Xleap's graphical editor allows manual cleanup before saving parm files. E.g. drag selected atoms, select a larger group, and use the simple minimizer to restore sanity. Note the minimizer does not take steric terms into account.
Bill
<div>-------- Original message --------</div><div>From: David A Case <case.biomaps.rutgers.edu> </div><div>Date:04/12/2015 5:57 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] intercalations </div><div>
</div>On Fri, Apr 10, 2015, Arjun Sharma wrote:
>
> The Polymer I built in xleap has some residues intercalating each other
> i.e bonds going through inside of aromatic ring of residues.
In general, there is nothing you can do inside Amber that will "fix" this.
LEaP makes some severe assumptions in adding in atoms that are not in the
input PDB file, and it is possible to get errors like this. You will need
to build an intial configuration that does not have these problems.
....dac
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Received on Sun Apr 12 2015 - 10:00:03 PDT
