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 amb2gmx.pl
Perl script to use this executable, not the one in $AMBERHOME/bin.
>
> In the am2gmx.py 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
pipe.
Try replacing "ambpdb.o" above with "/home/sbhakat/amber14/AmberTools/src/etc/ambpdb".
That will cause the amb2gmx.pl 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
amb2gmx.pl, and it is not a part of Amber.)
....dac
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Received on Wed May 20 2015 - 05:00:02 PDT
