AMBER Archive (2009)

Subject: [AMBER] Fwd: Group specification

From: Pavan G (pavanamber_at_gmail.com)
Date: Thu Oct 08 2009 - 13:30:09 CDT


Hello All,
I am trying to run a simulation with different restraint weights on
different groups of atoms in my system. I did find quite a few discussions
in the forum regarding this issue but none addressed the specific issue of
selecting certain atoms in a residue. I tried the following without success.
Kindly help me with your comments. If this has already been addressed I
apologize.

 /
 Hold protein tightly
 10.0
 ATOM :1-654_at_CA,N,C
 END
 Hold ligands
 5.0
 RES :LG1,LG2,LG3
 END
 Hold lipid tails lightly
 0.5
 ATOM :LIP_at_C1
 END
END

Error are mostly on the lines of
"GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
      GROUP 1 CONSISTS OF ATOMS -

      ***PROBLEMS WITH GROUPATOM***** 0 0 0 0 0 0 0
0 0 0 0 0 0*******

      Number of atoms in this group = 0
    ----- READING GROUP 2; TITLE:
  END
 rfree: End of file on unit 5

"

Thanks,
Pavan
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