Dear Hannes,
Yeah it is .pl not .py..silly mistake . I was also trying with acpype but I
am not sure how FESetup works especially at which point it converts AMBER
to Gromacs.
This is technically a very small issue but it seems to not so easy due to
various version changes and not upgrading some external tools as per the
upgraded version as well as not very good examples also.
Lets see,
SB
On Wed, May 20, 2015 at 12:04 PM, Hannes Loeffler <
Hannes.Loeffler.stfc.ac.uk> wrote:
> Not an answer to your question but I suspect the tool you are talking
> about is actually amb2gmx.pl (not .py). The code line you show looks
> very much like Perl to me.
>
> Amb2gmx.pl is actually deprecated and you are probably better off using
> tools like acpype or even FESetup.
>
> Cheers,
> Hannes.
>
>
> On Wed, 20 May 2015 11:52:02 +0200
> Soumendranath Bhakat <bhakatsoumendranath.gmail.com> wrote:
>
> > Dear Prof. D.A.Case,
> >
> > This might be very stupid.
> > 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
> > drwxrwxr-x 4 sbhakat sbhakat 4096 maj 20 10:51 build
> > -rw-rw-r-- 1 sbhakat sbhakat 4400 maj 20 09:17 forFIRSTsugar.o
> > -rw-rw-r-- 1 sbhakat sbhakat 7888 maj 20 09:17 forFIRSToutp.o
> > -rw-rw-r-- 1 sbhakat sbhakat 18896 maj 20 09:17 forFIRSTteth.o
> > -rw-rw-r-- 1 sbhakat sbhakat 12632 maj 20 09:17 forFIRSThbond.o
> > -rw-rw-r-- 1 sbhakat sbhakat 7112 maj 20 09:17 forFIRSTbond.o
> > -rw-rw-r-- 1 sbhakat sbhakat 14000 maj 20 09:17 forFIRSTtype.o
> > -rwxr-xr-x 1 sbhakat sbhakat 92000 maj 20 09:17 ambpdb.o
> >
> > 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";
> >
> > I am not getting what you mean by changing the path as the path
> > seems to be /home/sbhakat/amber14/bin/ambpdb
> >
> > Can you please explain a bit more. Just struggling with this as it is
> > not integrated with Amber 14.
> >
> > Your help will be highly appreciated.
> > Thanks for your time and support.
> >
> > Regards,
> > SB
> >
> >
> > On Tue, May 19, 2015 at 2:03 PM, David A Case
> > <case.biomaps.rutgers.edu> wrote:
> >
> > > On Tue, May 19, 2015, Soumendranath Bhakat wrote:
> > > >
> > > > I am trying to convert an AMBER topology to to GROMACS using
> > > > amb2gmx.py. But I get this error during running. Can some one
> > > > point out whats the problem in this case. Also amb2gmx seems to
> > > > work fine with Amber 11 but
> > > as
> > > > I generated PDB with TIP4Pew and FF14SB hence unfortumnately I
> > > > will not able to reproduce the trajectory. Is there any way to
> > > > fix this issue with amb2gmx in AmberTools15.
> > > >
> > > >
> > > > | ambpdb (C++) Version V15.00
> > > > Error: Option '-atm' is not yet supported.
> > >
> > > You can compile the "old" version of ambpdb in this way:
> > >
> > > cd $AMBERHOME/AmberTools/src/etc
> > > make ambpdb
> > >
> > > Then you would need to get this version of ambpdb to be first in
> > > you PATH, or modify the amb2gmx.py script to use this version and
> > > not the one in $AMBERHOME/bin.
> > >
> > > I'm not sure if this will work, since I've never used amb2gmx.py,
> > > but it should remove the error listed above.
> > >
> > > ....dac
> > >
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
>
>
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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 - 03:30:03 PDT
