Re: AMBER: mm_pbsa incorrect complex prmtop file

From: Neha Gandhi <>
Date: Thu, 10 Jul 2008 16:02:27 +0800


1. Use ptraj to extract receptor and ligand file separately from the
last trajectory. If you extract complex using ptraj, it ll not work as
ptraj will add atom number to TER, hence the pdb numbering and your
complex numbering dont match.
2. For complex use either ambpdb and then delete water molecules and
ions. Or the other option is use xleap instead of tleap. load receptor
first and then ligand from step 1. Then use edit receptor and then use
import unit. Then u can quit this. Then use savepdb receptor
3. Then you can create the prmtop file for the complex

I hope this helps,


On Thu, Jul 10, 2008 at 3:44 PM, xiaonan zhang <> wrote:
> 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

Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
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Received on Sun Jul 13 2008 - 06:07:21 PDT
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