From: Jason Swails <>
Date: Fri, 4 Oct 2013 07:07:07 -0400

On Fri, Oct 4, 2013 at 4:18 AM, Jacopo Sgrignani <> wrote:

> Dear all
> I'm trying to run MMPBSA Qm/MM calculations but I have some problems:
> 1) Even though I define ligand, receptor and complex qm-charge the
> program ignores these numbers and the qm-charge unspecified in the
> generated inputs file.
> 2) To overcome the first problem, I tried to use -make-mdins and then
> -use-mdins putting the charge in the generated files.
> However when I use the -use-mdins command the existing inputs are
> automatically deleted.
> I'm using my personal workstation so I can exclude automatic cleaning
> procedure.
> Can you help me?

I was able to reproduce your problem, and I have a solution that appears to
work. Please apply the attached patch, rebuild, and try again.
 The following steps should do everything (assuming you put mmpbsa.patch in

./update_amber --apply mmpbsa.patch
make -C AmberTools/src/mmpbsa_py install

That should reinstall without spending time rebuilding the rest
of Amber (which this patch does not affect).

If this patch works, I will roll it out as an update.

Thanks for the report!

Jason M. Swails
Rutgers University
Postdoctoral Researcher

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Received on Fri Oct 04 2013 - 04:30:04 PDT
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