Dear Prof. Case,
Ohh!!! I am stupid...yeah it worked..thank you so much for your explanation
and help.
Thanks & Regards,
SB
On Wed, May 20, 2015 at 1:33 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> 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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>
--
Thanks & Regards;
Soumendranath Bhakat
Research Assistant, Division of Biophysical Chemistry, CMPS, Lund
University, Sweden
Homepgae: https://cbiores.wordpress.com/
ResearchGate: https://www.researchgate.net/profile/Soumendranath_Bhakat2
Google Scholar: http://scholar.google.com/citations?user=Q1_nDMcAAAAJ&hl=en
Past: Molecular Modelling and Drug Design Research Group
Discipline of Pharmaceutical Sciences
UKZN, Westville
Weblink: http://soliman.ukzn.ac.za/Home.aspx
and Department of Pharmaceutical Sciences
Birla Institute of Technology, Mesra, India
in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
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Received on Wed May 20 2015 - 05:30:03 PDT
