Dear David,
Thank you for your input. Unfortunately, $AMBERHOME/src/protonate doesn't exist anymore in amber 14.
The only things I have found that is near to it are in the following folder:
$AMBERHOME/include/mtkpp/Molecule/, there is a file called protonate.h
$AMBERG+HOME/AmberTools/src/mtkpp/src/Molecule, there are files called protonate.h protonate.o and protonate.cpp
Furthermore if i do a grep search for pol_h , i don't find any file containing that specific string.
Is it possible that it has been removed or incorporated in another script?
Best regards,
Alistair Cerlier
--------------------------------------------
On Fri, 12/2/16, David A Case <david.case.rutgers.edu> wrote:
Subject: Re: [AMBER] question about pol_h in ambertool15
To: "Thibaud von Erlach" <thibeli.yahoo.com>, "AMBER Mailing List" <amber.ambermd.org>
Date: Friday, December 2, 2016, 4:54 AM
On Thu, Dec 01, 2016,
Thibaud von Erlach wrote:
>
>
I am trying to install a program which following the
programmer would
> need amber15 (since
amber15 doesn't exist I suppose they refer to
> ambertools15) and more specifically the
program would need the following
>
scripts: protonate and pol_h. After looking a bit at the
different
> version we have installed
here, there indeed seem to be a protonate
> script in ambertool15 but there is no
trace whatsoever of a pol_h script
> ...
(After digging a little bit deeper, I have found that it
exists in
> our version of amber10 and
amber9 but not in the versions after)
>
So my question is:
> does pol_h still
exist for ambertools15 or has it been removed? or has
> it been replaced by something
else?
The code is
still there, but we don't build by default it any more,
since
the "standard" Amber
workflow now uses reduce.
You can do this:
cd
$AMBERHOME/AmberTools/src/protonate
make install
and you will get pol_h and other programs that
deal with hydrogens.
...hope this helps....dac
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Received on Fri Dec 02 2016 - 00:30:02 PST
