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

[sucharita dey]

Thanks Rashmi. Finally, I have been able to install g_mmpbsa.  Apart from
the gmx lib files there were issues in installing APBS as well, took a
quite amount of time to find the source code of that version that has the
lib files needed for g_mmpbsa.
Thanks anyways,
Sucharita



On Mon, Jun 16, 2014 at 9:39 PM, Rashmi <rashkush at gmail.com> wrote:

> 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
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > 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.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>