AMBER: MM_PBSA doesn't terminate

From: Khaled Barakat <>
Date: Tue, 21 Oct 2008 10:58:12 -0600


I am trying to run MM_PBSA of AMBER10 to decompose the binding energy between a protein and
DNA molecule. The protein contains a ZN atom. I went through the mailing list and found two entries
discussing this problem. They suggested to set RADIOPT = 0 and the NPOPT =1, in order to force
MM_PBSA to read the ZN parameters from the prmtop files. This solution worked for the Binding
Energy calculation, however, when I try to decompose the Energy into residue contributions,
MM_PBSA doesn’t terminate and I am getting the following errors (see under my signature).

Thanks in advance,
With my best regards

No values for PB_SPBSOL existing -> Skipping
    Processing PB TPBSOL
        Doing 1 PB TPB
        Doing 1 GB TGBSUR
    No values for GB_TGBSUR existing -> Skipping
    Processing PB SPBSOL
        Doing 1 PB SPB
        Doing 1 GB SGBSUR
    No values for GB_SGBSUR existing -> Skipping
    Processing PB TPBTOT
        Doing 1 PB TPBSOL
    No values for PB_TPBSOL existing -> Skipping
    Processing PB BPBTOT
        Doing 1 PB BPBSOL

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Received on Wed Oct 22 2008 - 05:10:49 PDT
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