[AMBER] MMPBSA Calculation Error: Order of protein and ligand

From: M RCC <mkr3j2c1.gmail.com>
Date: Tue, 19 Feb 2019 22:47:07 +0530

Dear Amber Users,
I am facing an error in PBSA calculation. and I need a few clarifications.

My system contains the coordinates of following in the specified order.
Protein + ligand + cofactor
MD simulation running well without any error.
While performing MMPBSA calculation I have prepared the topology as follows
complex: *Protein + ligand + cofactor *
receptor: *Protein + ligand + cofactor*
ligand: *ligand*

While starting the calculation it gives an error with the complex topology.
I checked the mdout files. It says NATOM mismatch error. I have comverted
the prepared topology & crd files of complex and receptor to PBD files and
it shows the equal number of atoms.

What am possibly missing here?
Does it bcoz of the order of the protein and ligand coordinates?
AMBER mailing list
Received on Tue Feb 19 2019 - 09:30:02 PST
Custom Search