AMBER Archive (2005)

Subject: AMBER: Sander: idecomp

From: lei jia (jial_at_broyde.nyu.edu)
Date: Tue Mar 15 2005 - 13:45:47 CST

Dear Amber users,

I am using MM-PBSA generated sander input file to calculate the
component interactions of a group of atoms. I had no problem to
calculate them on the residue level by using the RES card. I wonder if I
can do that on the atom level by using the ATOM card in the group
specification section. If not, what can I do to calculate the
interactions between the whole molecule and several atoms belong to the
molecule. Thanks a lot!

Lei

Here are my input files and error messages from the output:
#############################################################
File generated by mm_pbsa.pl. Using MM
 &cntrl
  ntf = 1, ntb = 0, dielc = 1,
  idecomp= 1,
  igb = 2, saltcon= 0,
  offset = 0.09, extdiel= 78.5,
  gbsa = 0, surften= 1.0,
  cut = 99999.0, nsnb = 99999,
  scnb = 2.0, scee = 1.2,

  imin = 1, maxcyc = 1, ncyc =0,
 &end
Residues considered as REC
RRES 1 22
END
Residues to print
ATOM 173 182
END
END
######################################################
    ----- READING GROUP 2; TITLE:
 Residues to print
      ***PROBLEMS WITH GROUPATOM 173 182 0 0 0 0 0
0 0 0 0 0 0 0*******

      Number of atoms in this group = 0

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