HI everybody,
I am doing restrained (NMR restraints) simulated annealing on a
portion of larger protein complex. I want to 'freeze' most of the
protein and study only part of the complex (ibelly =1). I am doing this
in vacuo (igb = 3).
I have tried two variations: 1). belly dynamics on the active site
residue side chains and ligands, and 2). belly dynamics on all side
chains and ligands.
Sander (amber ver 6) keeps complaining that the group must be at the
beginning of the molecule file if igb>0 is used.
Any ideas?
Thanks in advance for any help.
Richard Kho
Postdoc
Triad Therapeutics, Inc.
San Diego, CA 92126
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part of input file SA.in:
group 1
50
FIND
* * 3 *
* * B *
* * S *
* * E *
SEARCH
RES 1 826
FIND
* * * *
SEARCH
RES 827 827
END
END
Part of output:
LOADING THE BELLY ATOMS AS GROUPS
----- READING GROUP 1; TITLE:
group 1
ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE
INCLUDED IN GROUP BELOW
GRAPH NAME = * SYMBOL = * TREE SYMBOL = 3 RESIDUE
TYPE = *
GRAPH NAME = * SYMBOL = * TREE SYMBOL = S RESIDUE
TYPE = *
GRAPH NAME = * SYMBOL = * TREE SYMBOL = B RESIDUE
TYPE = *
GRAPH NAME = * SYMBOL = * TREE SYMBOL = E RESIDUE
TYPE = *
GRP 1 RES 1 TO 826
ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE
INCLUDED IN GROUP BELOW
GRAPH NAME = * SYMBOL = * TREE SYMBOL = * RESIDUE
TYPE = *
GRP 1 RES 827 TO 827
Number of atoms in this group = 10205
----- END OF GROUP READ -----
When igb>0, the moving part must be at the
start of the molecule. This does not seem
to be the case here.
natbel,i,igroup(i) = 10205 10207 1
----- READING GROUP 1; TITLE:
group 1
ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE
INCLUDED IN GROUP BELOW
GRAPH NAME = * SYMBOL = * TREE SYMBOL = M RESIDUE
TYPE = *
GRP 1 RES 1 TO 826
ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE
INCLUDED IN GROUP BELOW
GRAPH NAME = * SYMBOL = * TREE SYMBOL = * RESIDUE
TYPE = *
GRP 1 RES 827 TO 827
Number of atoms in this group = 2531
----- END OF GROUP READ -----
When igb>0, the moving part must be at the
start of the molecule. This does not seem
to be the case here.
natbel,i,igroup(i) = 2531 2533 1
Received on Fri Mar 15 2002 - 16:59:23 PST
