Re: [AMBER] question about pol_h in ambertool15

From: Thibaud von Erlach <thibeli.yahoo.com>
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 <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 it been replaced by something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
 
 

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 02 2016 - 00:30:02 PST
Custom Search