I am not sure what you mean by this. Both tools call leap so any force
field leap can handle can be handled by the tools. FESetup does the
conversion as soon as you invoke the MD engine for Gromacs but I have
this documented.
On Wed, 20 May 2015 12:15:18 +0200
Soumendranath Bhakat <bhakatsoumendranath.gmail.com> wrote:
> I am not sure if acpype will be efefctive as in ACPYPE only some
> versions o FF99SB force field is integrated
> http://svn.code.sf.net/p/ccpn/code/branches/stable/ccpn/python/acpype/ffamber_additions/
> whereas we used FF14 force field to generate the files.
>
> On Wed, May 20, 2015 at 12:13 PM, Soumendranath Bhakat <
> bhakatsoumendranath.gmail.com> wrote:
>
> > 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
> >> > >
> >> > >
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >
> >> >
> >> >
> >> >
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> 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/
> >
> >
>
>
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Received on Wed May 20 2015 - 03:30:05 PDT
