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

[sucharita dey]

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
> > --
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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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