restraining atoms

From: Ioana Cozmuta <ioana_at_nas.nasa.gov>
Date: Wed 16 Oct 2002 10:56:10 -0700 (PDT)

Hi,

I am trying to restrain some of the heavy atoms in the structure

****************************
Restrain the 7AHL heavy atoms I
5000.0
FIND
 * CA * *
 * CB * *
 * CD * *
 * CD1 * *
 * CD2 * *
 * CE * *
 * CE1 * *
 * CE2 * *
 * CE3 * *
SEARCH
RES 1 2051
END
**********************

but I see in the output file that sander is not able to recognize the
three character definition of the atoms (CD1, CD2, CE1, CE2, CE3)

**************************************
     GROUP 1 HAS HARMONIC CONSTRAINTS 5000.00000
    ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED
IN GROUP BELOW

     GRAPH NAME = * SYMBOL = CA TREE SYMBOL = * RESIDUE TYPE = *
      GRAPH NAME = * SYMBOL = CB TREE SYMBOL = * RESIDUE TYPE = *
      GRAPH NAME = * SYMBOL = CD TREE SYMBOL = * RESIDUE TYPE = *
      GRAPH NAME = * SYMBOL = CD TREE SYMBOL = * RESIDUE TYPE = *
      GRAPH NAME = * SYMBOL = CD TREE SYMBOL = * RESIDUE TYPE = *
      GRAPH NAME = * SYMBOL = CE TREE SYMBOL = * RESIDUE TYPE = *
      GRAPH NAME = * SYMBOL = CE TREE SYMBOL = * RESIDUE TYPE = *
      GRAPH NAME = * SYMBOL = CE TREE SYMBOL = * RESIDUE TYPE = *
      GRAPH NAME = * SYMBOL = CE TREE SYMBOL = * RESIDUE TYPE = *
 GRP 2 RES 1 TO 2051
      Number of atoms in this group = 1260
****************************************

What is the correct way to define these atoms so that sander recognizes
them (the names are assigned in Leap).

Thank you,
Ioana
Received on Wed Oct 16 2002 - 10:56:10 PDT
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