AMBER Archive (2004)

Subject: Re: AMBER: restraintmask and ambmask

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Thu Apr 22 2004 - 07:27:38 CDT

Oliver Hucke wrote:

> I am trying to use the restraintmask keyword of amber8 to apply
> restraints to all residues which are further than 5.0A away from a
> specific residue:
>
> restraintmask = :534 >:5.0,
>
> This line lets sander crash with
> "too many values for NAMELIST variable, unit 5 ..."

You have to enclose the expression into quotes, as you did below.

> Whe I use
>
> restraintmask = ":534 >:5.0",
>
> sander runs but in the output file I find:
> "Mask :534 >:5.0; matches 0 atoms
>
> With ambmask the selection string ":534 >:5.0" works.
>
> Is the complete ambmask syntax not yet available in sander8?

that's weird - sander uses the same parsing module (the same code) as
ambmask does. Is it possible that you send me (rather directly than to
the list if they're too big) your inputs - obviously coordinates and
topology would be most useful, but sander input would help too...

-Viktor

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