Re: [AMBER] Problem with amb2gmx in AmberTools 15

From: David A Case <>
Date: Wed, 20 May 2015 07:33:46 -0400

On Wed, May 20, 2015, Soumendranath Bhakat wrote:
> As per your advise I executed the above mentioned command. It generated
> some files especially the following
> -rwxrwxr-x 1 sbhakat sbhakat 136119 maj 20 11:11 ambpdb

The file above is the "old" ambpdb executable file. You want the
Perl script to use this executable, not the one in $AMBERHOME/bin.

> In the there is an option to add the path which seems to me
> here my $command = "cat $crd_filename | ambpdb.o -atm -p
> $prmtop_filename > $pdb_filename";

This doesn't make sense (to me, at least.) "ambpdb.o" is a compiled object
file (not an executable file) and it would not make sense to have that in a

Try replacing "ambpdb.o" above with "/home/sbhakat/amber14/AmberTools/src/etc/ambpdb".
That will cause the script to use the "old" version of ambpdb,
which is what you want.

(I'll note again that I'm just giving general advice here--I've never used, and it is not a part of Amber.)


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Received on Wed May 20 2015 - 05:00:02 PDT
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