AMBER Archive (2005)

Subject: Re: AMBER: nmode with ibelly

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 08 2005 - 23:30:01 CDT

On Wed, Jun 08, 2005, Martin Sippel wrote:
>
> Using ptraj's strip option, I get
> polypeptides without proper termini (missing OXT) due to truncation of
> adjacent amino acids;

If you remove the PdbResMap commands from your leaprc file, LEaP will not
try to add the OXT atoms. What you are trying is a very non-standard option,
so you should expect to have to play around a little to get it to work.

...good luck...dac

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