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
