Dear Hannes,
Ya acpype also works fine. Will try FESetup also.
Problem solved..thanks to you and Prof. Case.
/SB
On Wed, May 20, 2015 at 5:44 PM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> 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/
>
>
--
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 - 10:00:02 PDT
