Re: [AMBER] question about pol_h in ambertool15

From: David A Case <>
Date: Thu, 1 Dec 2016 21:54:30 -0500

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 it been replaced by something else?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 - 19:00:02 PST
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