attached mail follows:
Dear Amber expert,
I try to run minimization with some restraint ligand atoms and some residues.
The input file is below.
Initial minimization in solvent (water)
&cntrl
imin = 1,
maxcyc = 300,
ncyc = 300,
ntb = 1,
ntpr = 10,
cut = 12,
ntr = 1
/
Keep residue 71 fixed with restraints
5000.0
RES 71
END
Keep residue 83 fixed with restraints
5000.0
RES 83
END
Keep residue 120 fixed with restraints
5000.0
RES 120
END
Keep residue 117 fixed with restraints
5000.0
RES 117
END
Keep residue 329 fixed with restraints
5000.0
RES 329
END
Restraint atom specification in ligand 535
5000.0
FIND
* C2 * *
* N21 * *
* C3 * *
SEARCH
RES 535
END
END
For residue restraint, there are no problem, but for ligand atom
restraint, in the output file it appears like that:
----- READING GROUP 6; TITLE:
Restraint atom specification in ligand 535
GROUP 6 HAS HARMONIC CONSTRAINTS 5000.00000
ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE
INCLUDED IN GROUP BELOW
GRAPH NAME = * SYMBOL = C2 TREE SYMBOL = *
RESIDUE TYPE = C51
GRP 6 RES 535
Number of atoms in this group = 0
----- END OF GROUP READ -----
It means that, ligand atoms are not recognized. What should I do to
make the restraint in some atoms of the ligand?
Thanks in advance.
Regards,
Nguyen Thanh Binh
PhD student, BII, Singapore.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 10 2012 - 09:30:04 PDT
