Can you print your error log here to assess it better?
NATOM mismatch error usually means you didn't prepare your top files
correctly.
Are you using ante-MMPBSA.py to prepare the top files?
Jubilant
On Tue, Feb 19, 2019 at 11:23 AM M RCC <mkr3j2c1.gmail.com> wrote:
> 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?
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--
Thanks,
Sundar Thangapandian
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Received on Tue Feb 19 2019 - 10:00:03 PST
