In theory, you should be able to use a chloride ion as a ligand. It's more
a question of if you think MMPBSA will provide you useful results, which is
something I'm not too clear on. That's a topic you might want to take a
look through the literature on to see how they interpreted the results. At
the very least, I'd be cautious in going over your outputs to make sure
they make sense.
LengthError: length mismatch in energy vectors
> Error occured on rank 0.
> Exiting. All files have been retained.
I've never run into this problem before, but a search through the mailing
list brings up a possible explanation of what's going on (
http://archive.ambermd.org/201311/0030.html).
Best,
Kenneth
On Mon, Apr 13, 2015 at 8:42 AM, wjli <wenjuanli93.gmail.com> wrote:
> Thanks for your patience.
>
> I think I ignored a crucial question:can ion be ligand to caculate the
> free energy change？（More commonly in MMPBSA is small molecule or
> protein）.In my situation,ligand is chloride ion.
>
> And I even try to run MD and MMPBSA.py without force field developed by
> MCPB (so no bad atom type),there is still error:
> LengthError: length mismatch in energy vectors
> Error occured on rank 0.
> Exiting. All files have been retained.
>
> Do you have any advices for me?
>
> Best wishes.
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Apr 13 2015 - 11:00:02 PDT
