AMBER Archive (2002)

Subject: (no subject)

From: Bill Ross (photoriot_at_yahoo.com)
Date: Tue Apr 23 2002 - 14:30:58 CDT

> I am having a problem with the DME function in
> Carnal in AMBER6. I am trying to obtain essentially
> an RMS value for the Calpha atoms in my MD
silumation
> for comparison with the Bvalues in the crystal
> structure. The program accepts the input file, but
> gives junk for an output.

You are not defining a legal DME command:
"DME compares intra-group distances in one
conformation to those in another conformation."
 
> GROUP grp7 ((ATOM NAME CA) & (RES 7));
> ...
> DME dmeid7 grp7 si ref_set;
 
The group consists of one atom, so there can be no
intra-group distances. I'll update Carnal to trap
this input error. I'm guessing that a single DME
(or RMS FIT) on a group like this is what you want:

   GROUP grp1 (ATOM NAME CA);
or
   GROUP grp1 ((ATOM NAME CA) & (RES 2-10));

Bill Ross

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