IC.
thanks a lot for this helpful advices.
There is some crystal waters in the input protein, probably they are not
handle correctly? I will check it .
best
Albert
On 04/03/2013 04:00 PM, Bill Miller III wrote:
> This could be due to a mismatch between the topology files that you
> provided and the trajectories created by MMPBSA.py from your original
> trajectory. You should try visualizing the trajectories made by MMPBSA.py
> with their corresponding topology files that you provided to see if they
> look right. If they do not, it is likely because there is some mismatch
> between the residues in the topology files, possibly ions or other residues
> that were unintentionally removed? You can also check the mdout files
> created by MMPBSA.py to see if they provide any helpful messages.
>
> -Bill
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 03 2013 - 07:30:03 PDT
