[gmx-users] g_mmpbsa: MM-PBSA method for GROMACS

[Rashmi]

Hi Sucharita,

Please post as new thread or in g_mmpbsa forum.

You could install Gromacs at new location using followings with cmake:

-DCMAKE_INSTALL_PREFIX=/to/custom/path
-DBUILD_SHARED_LIBS=OFF
-DGMX_GPU=off

Then, g_mmpbsa can be compiled using this Gromacs. We will fix this
installation issue in future version.

​
​
With Regards,
Rashmi​



On Mon, Jun 16, 2014 at 11:41 AM, sucharita dey <sucharita.dey at gmail.com>
wrote:

> Hi Rashmi,
>
> I am facing difficulty in installing the tool you mentioned g_mmpbsa. I am
> giving this command:
>  ./configure --enable-gmx46 --with-gmx-include=/usr/local/gromacs/include
> --with-gmx-lib=/usr/local/gromacs/lib
> ................
> configure: error: Could not find /libgmx.a library file
>
> I found in my gromacs4.6.3 lib folder '/usr/local/gromacs/lib'  the files
> are 'libgmx.so', 'libgmxana.so' etc.. instead of 'libgmx.a' or
> 'libgmxana.a'.
> Please suggest how do I get this files without hampering my installed
> gromacs as presently a number of programs are running.
>
> Thanks,
> Sucharita
>
>
> On Fri, Jun 13, 2014 at 10:32 PM, Rashmi <rashkush at gmail.com> wrote:
>
> > Dear Prof. David van der Spoel,
> >
> > Thank you very much for considering g_mmpbsa for the GROMACS repository.
> We
> > have a discussion on the same and will try to patch g_mmpbsa in the
> > repository. Presently, we do not know how to integrate compilation
> > procedure of g_mmpbsa with the GROMACS package as APBS libraries are
> > required during compilation and Fortran compiler are required for the
> > linking.
> >
> > Since I am travelling these days, hope we could able to work on the same
> in
> > a month and so.
> >
> > With Regards
> > Rashmi Kumari
> > PhD Student
> > School of Computational and Integrative Sciences
> > Jawaharlal Nehru University
> > New Delhi, India.
> >
> >
> >
> >
> >
> > On Tue, Jun 10, 2014 at 1:42 AM, David van der Spoel <
> spoel at xray.bmc.uu.se
> > >
> > wrote:
> >
> > > On 2014-06-09 21:17, Rashmi wrote:
> > >
> > >> Dear GROMACS users,
> > >>
> > >> We have developed a new tool,
> > >> *​​g_mmpbsa* for GROMACS to carry out the MM-PBSA calculations. It
> uses
> > >> APBS libraries for the Poisson-Boltzmann calculations.
> > >> ​
> > >>
> > >> ​Features:
> > >>
> > >>     - ​​
> > >>     Include SASA, SAV and WCA
> > >>     ​-like​
> > >>     non-polar models
> > >>     - It inherits threading (OpenMP) functions from APBS
> > >>     - Simultaneously calculate
> > >>     ​​
> > >>     energy contribution
> > >>     ​s​
> > >>     of residue
> > >>     ​s​
> > >>     to binding
> > >>     ​
> > >>
> > >>
> > >> Details of this
> > >> ​ tool​
> > >> are given in the following link:
> > >> ​
> > >> http://rashmikumari.github.io/g_mmpbsa/​
> > >>
> > >> Its implementation and testing are discussed in the following
> > publication:
> > >> ​
> > >> http://pubs.acs.org/doi/abs/10.1021/ci500020m​
> > >>
> > >> We would appreciate for suggestions
> > >> ​ ​
> > >> regarding
> > >> ​ ​
> > >> improvment of
> > >> ​ ​
> > >> this tool.
> > >>
> > >> With Regards,
> > >> Rashmi
> > >> ​ ​
> > >> Kumari
> > >> School of Computational and Integrative Sciences,
> > >> Jawaharlal Nehru University,
> > >> New Delhi
> > >> ​ ​
> > >> 110067, India.
> > >>
> > >>  Why not upload a patch to http://gerrit.gromacs.org ?
> > >
> > >
> > > --
> > > David van der Spoel, Ph.D., Professor of Biology
> > > Dept. of Cell & Molec. Biol., Uppsala University.
> > > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> > > spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> > > --
> > > Gromacs Users mailing list
> > >
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> > >
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> > >
> >
> >
> >
> > --
> > With Regards,
> >
> > Rashmi Kumari
> > Visting Student
> > School of Chemistry and Molecular Biosciences (MD group)
> > The University of Queensland
> > St. Lucia, Brisbane, QLD 4072, Australia
> > Contact No.- +61 434872368.
> > --
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