Re: [AMBER] Error in making and running xleap

From: Jason Swails <>
Date: Tue, 26 Aug 2014 07:30:45 -0400

On Tue, 2014-08-26 at 13:16 +0500, wrote:
> Hello
> The "loacl" was a typing mistake.
> I again installed amber14 (in Downloads directory) using commands
> "./configure gnu" and "make install" and set the AMBERHOME to `pwd`.
> The "dat" directory was not made neither the "dat text file" was made.
> So I manually made a new directory named "dat" and again ran the
> command "make install". The terminal showed that the installation is
> complete.
> make[2]: Leaving directory
> `/home/ammarah/Downloads/amber14/AmberTools/src/nmode'
> Installation of AmberTools14 serial is complete at Tue Aug 26 12:55:53
> PKT 2014.
> make[1]: Leaving directory `/home/ammarah/Downloads/amber14/AmberTools/src'
> ==============================================================
> /home/ammarah/Downloads/amber14/src/Makefile not found, or -noamber was set.
> This is expected if you do not have Amber14.
> ==============================================================
> But again when I was trying to run xleap in the
> "/Downloads/amber14/AmberTools/bin" directory via "./xleap", it gave
> the following error.
> -I: Adding /home/ammarah/Downloads/amber14/dat/leap/prep to search path.
> /home/ammarah/Downloads/amber14/dat/leap/prep: No such file or directory
> Other bin files are running. For example when I run the command
> "./antechamber" it lists its usage (e.g., -i, -fi, -o, -fo etc etc)
> Any suggestions please?

So all you've done is create a blank dat directory in AMBERHOME. All
this will do is (maybe) change the error messages you receive -- the
only reason xleap is looking in the dat/ directory is because it needs
some of the files inside ;). The fact is, $AMBERHOME/dat is unpacked
from the AmberTools 14 release tarball. If that directory is not
present in your $AMBERHOME, it's either because you received a copy of
AmberTools from somebody that didn't package up the whole distribution
(or you made a copy, but didn't copy the whole distribution), you
deleted that directory immediately after unpacking the tarball, or you
specified exactly what to unpack from the AmberTools tarball and omitted
the dat directory.

There may be some other possibilities, but the point is something went
wrong before you even started. You should download a _fresh_ copy of
AmberTools 14 from here:

Install the source code per the instructions (ex.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Aug 26 2014 - 04:30:02 PDT
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