AMBER Archive (2009)

Subject: Re: [AMBER] entangle-less building

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Jun 10 2009 - 17:38:31 CDT

> can anybody please help me to build entangle-less polymer like dendrimer. I=
> am using my own residues but when I sequence them they get entangled.

The 'sequence' cmd in leap does not avoid steric overlap.
You may be best off with loading from a pdb with a conformation
that you have prepared in the molecular editor of your choice.

Or clean it up in xleap. Minimization may help (leap's minimization
doesn't know about vdw, btw).

Bill

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