Re: [AMBER] question about pol_h in ambertool15

From: Anon <>
Date: Fri, 2 Dec 2016 00:13:20 -0300

This directory no longer exists, I'm looking for it, too. I appreciate if
anyone could help.

anonimo.Debian:~/Documents/gen/amber14/AmberTools/src$ ls
addles/ cphstats/ mmpbsa_py/ reduce/
amberlite/ cpptraj/ mtkpp/
amgauss/ emil/
nab/ sander/
antechamber/ etc/ netcdf-4.3.0/ saxs/
arpack/ FEW/ netcdf-fortran-4.2/ sebomd/
blas/ fftw-3.3/
nmode/ semantics/
boost-1.38.0/ gbnsr6/ nmr_aux/ sff/
byacc/ include/
nss/ sqm/
c9x-complex/ lapack/ paramfit/
cifparse/ leap/ parmed/
configure lib/
pbsa/ xtalutil/
configure2 Makefile ptraj/
configure_mpich mdgx/ pymsmt/
configure_openmpi mm_pbsa/ pysander/

On Thu, Dec 1, 2016 at 11:54 PM, David A Case <>

> 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 it been replaced by something else?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 Thu Dec 01 2016 - 19:30:03 PST
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