Re: [AMBER] QM/MM MMPBSA

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 4 Oct 2013 07:07:07 -0400

On Fri, Oct 4, 2013 at 4:18 AM, Jacopo Sgrignani <sgrigna.gmail.com> 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 MMPBSA.py, and try again.
 The following steps should do everything (assuming you put mmpbsa.patch in
$AMBERHOME):

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

That should reinstall MMPBSA.py 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

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher



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