AMBER Archive (2004)

Subject: Re: AMBER: ptraj questions

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Sun Oct 31 2004 - 11:06:54 CST

I think that nofit is ignored and a best-fit is always performed, maybe
Tom Cheatham can clarify this...
Carlos

Oliver Hucke wrote:

>
>
> Carlos Simmerling wrote:
>
>> I think nofit is broken, so overlap of 1 residue will always be small.
>>
>
> So, "nofit" should not be used at all? Is this valid for ptraj of amber8?
>
> Thanks,
> Oliver
>
> ________________________________________________________________
>
> Oliver Hucke, Dr.
> Biomolecular Structure Center Health Sciences Building - K418C
> Dept. of Biochemistry 1959 NE Pacific St.
> University of Washington phone: (206) 685 7046
> Box 357742 fax : (206) 685 7002
> Seattle, WA 98195-7742 email: ohucke_at_u.washington.edu
> ________________________________________________________________
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