Re: [AMBER] question about pol_h in ambertool15

From: Thibaud von Erlach <>
Date: Fri, 2 Dec 2016 08:24:45 +0000 (UTC)

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 <> wrote:

 Subject: Re: [AMBER] question about pol_h in ambertool15
 To: "Thibaud von Erlach" <>, "AMBER Mailing List" <>
 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
> 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 it been replaced by something
 The code is
 still there, but we don't build by default it any more,
 the "standard" Amber
 workflow now uses reduce.
 You can do this:
    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
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