AMBER Archive (2003)

Subject: Re: AMBER: Cutress %cmass error

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Nov 19 2003 - 13:51:04 CST

> I am trying to define a group in carnal that is 10A from the center of
> mass of my ligand. Here is my carnal file:
>
> CUTRES c1 g1%cmass 10.0 ;
> .............^
> Error in stdin line 7: CUTRES: expected cutoff
> Last token was %
>
> Does anyone know why it is terminating at the "%"?
 

Per the manual, this usage is not supported. You can use a groupid
(without a '%' modifier) to find residues with atoms within the cutoff
from atoms in the group.

Allowing the '%cmass' and '%center' options makes some sense, and
I am looking at implementing it. One issue raised is whether to
allow residues in the group itself to appear; in the current
distance-from-group version they are not output. Does anyone have
an opinion?

Bill Ross

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu