AMBER: MM_PBSA doesn't terminate

From: Khaled Barakat <>
Date: Wed, 22 Oct 2008 09:27:55 -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
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Wed Oct 22 2008 - 19:58:54 PDT
Custom Search