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

[Rashmi]

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.