AMBER Archive (2006)

Subject: Re: AMBER: any work-around for 80 character mask string limit?

From: David A. Case (
Date: Tue Aug 01 2006 - 16:37:36 CDT

On Tue, Aug 01, 2006, Tanya Johannsen wrote:
> I have a very long, complicated list of residues that
> I would like to restrain using ntr=1 during
> minimization. There is no way that I can define this
> list of residues in 80 characters or less,

You can do two things:

1. Use the "old style" restraints, i.e. using the group syntax, without the

2. Apply the attached patch (only lightly tested) to
$AMBERHOME/src/sander/findmask.f, and re-compile. This ups the size of the
string to 256 character.

...good luck....dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to