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
>> > >
>> >
>> >
>> >
>>
>>
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>> 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 - 03:30:04 PDT
