Dear Ioana,
are you sure CD? are atom TYPES? I suppose these are names. TYPES should be
two character long...... Yours are maybe NAMES ( i.e. the 1st column?)
Hope this helps,
Martin Lepsik
> 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 - 23:56:17 PDT
