AMBER Archive (2003)

Subject: AMBER: Restraints

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Thu Nov 06 2003 - 14:28:09 CST

Hi Amber users.

What I am trying to do is simple, but yet there appears to be a problem. I am trying to restrain one amino acid in the protein (His203), the iron atom of my heme group and the oxygen atom in residue 554 (a ligand bound at active site). I write in the following at the end of a namelist:

&end

Restrain iron atom

100

FIND

* FE * *

SEARCH

RES 553 553

END

Restrain oxygen atom of Ligand

100

FIND

* OH * *

SEARCH

RES 554 554

END

Restrain His203 residue

100

RES 176

END

END

Here is the the OUTPUT file:

GROUP 2 HAS HARMONIC CONSTRAINTS 100.00000

ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED IN GROUP BELOW

GRAPH NAME = * SYMBOL = OH TREE SYMBOL = * RESIDUE TYPE = *

GRP 2 RES 554 TO 554

Number of atoms in this group = 0

It says that no atoms in group 2 are being restrained. The other restraints are fine. I cannot figure out why.

Does anyone else know why?

P.S. I have made sure that "OH" is the atom type in both Leap and in my pdb files for this ligand.

Thanks

Steve

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