[AMBER] specific atom restraint

From: Thanh Binh NGUYEN <nguyentb.bii.a-star.edu.sg>
Date: Sat, 11 Aug 2012 00:09:47 +0800

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.


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Received on Fri Aug 10 2012 - 09:30:04 PDT
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