AMBER Archive (2008)

Subject: AMBER: mm_pbsa incorrect complex prmtop file

From: xiaonan zhang (
Date: Thu Jul 10 2008 - 02:44:58 CDT

Dear All
      As a novice in AMBER, I made a silly mistake about MM-PBSA analysis.
As I am preparing the prmtop and inpcrd files
for the system. I didn't prepare three separate complex/receptor/ligand
topology files. Now I have the trajectory ready but without
these files.. I tried to fix this by preparing these files from pdb files
again. Basically, I made the complex topology file directly from
pdb file and cut out receptor and ligand part respectively in the original
pdb file into new pdb file and prepare their topology file.
      Unfortunately, this seems does not work. After running the mm_pbsa
script, the error message was:
  checking sanity
    Checking GENERAL
    Implicit SAS calc by sander
    COMPT must be specified (correctly)

I want to ask are there any other way for the salvage?
Can I load the promtop and inpcrd into xleap and edit them and then save the
three needed topology files??

Many Thanks!

Xiaonan Zhang

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