AMBER Archive (2004)

Subject: AMBER: mm_pbsa question

From: hj zou (hjzou_at_iris3.simm.ac.cn)
Date: Wed Feb 18 2004 - 21:22:00 CST

dear amber users,
    I'm performing mm_pbsa simulation.
    I have generated the snapshots sucessfully. When I calculate the binding energy, I get three all.out files for ligand,receptor and the complex properly. However there is no statistics.out file.
    The log file shows the following message:
"No values for PB_PBSOL existing -> Skipping......."
   and it stops at "cacl delta"
   Following information is displayed on the screen:
   "make_cones() MAXTOR_PROBE exceeded
    make_cones() MAXTOR_PROBE exceeded
    make_cones() MAXTOR_PROBE exceeded
    Use of uninitialized value at /userdata/cluo/amber7/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1203.
    Use of uninitialized value at /userdata/cluo/amber7/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1203.
    No data for 0+0 MS SURF 0 "

    According to Holger's suggestion,I Comment the lines
"unlink $sanout", "unlink $delphiout", "unlink $mol"

   Here is the information in mm106_rec.mslog.99:
           2043 atoms read

       WARNING: 4 cusps intersection: not trimmed yet
       WARNING: 3 cusps intersection: not trimmed yet
       surface area = 7013.008
  

       Any suggestions?
      Thank you in advance.
      best regards

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