Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

[neha chaudhary]

Hi,

I tried to compile g_mmpbsa with APBS but no success. I am facing the
following error while cmake:

-- Found z library: /usr/lib/x86_64-linux-gnu/libz.so
CMake Error at cmake/FindGROMACS.cmake:203 (list):
  list index: 2 out of range (-2, 1)
Call Stack (most recent call first):
  src/CMakeLists.txt:62 (find_package)


-- Found Gromacs include directory: /usr/local/gromacs/include
-- Configuring incomplete, errors occurred!

Please help.

Thanks.

*Neha*




On Wed, Aug 30, 2017 at 10:42 AM, neha chaudhary  wrote:

> Hi,
>
> I will download and install APBS and try again.
>
> I have already tried pre-compiled version of g_mmpbsa from the link you
> suggested.
>
> Thanks
>
> Best Regards,
>
> *Neha*
>
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himachal Pradesh,
>
>
>
>
>
> On Wed, Aug 30, 2017 at 10:38 AM, Nikhil Maroli 
> wrote:
>
>> Hell,
>>
>> Download APBS and install it then use the binary package of g_mmpbsa. or
>> see here:
>>
>> Pre-compiled executable program
>>
>> Pre-compiled program does not require any external library or GROMACS and
>> APBS package. These programs are standalone and without any dependency.
>> Download, extract and use it.
>>
>>
>> http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html
>> --
>> 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-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

[neha chaudhary]

Hi,

I will download and install APBS and try again.

I have already tried pre-compiled version of g_mmpbsa from the link you
suggested.

Thanks

Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Aug 30, 2017 at 10:38 AM, Nikhil Maroli  wrote:

> Hell,
>
> Download APBS and install it then use the binary package of g_mmpbsa. or
> see here:
>
> Pre-compiled executable program
>
> Pre-compiled program does not require any external library or GROMACS and
> APBS package. These programs are standalone and without any dependency.
> Download, extract and use it.
>
>
> http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html
> --
> 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-requ...@gromacs.org.
>
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Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

[Nikhil Maroli]

Hell,

Download APBS and install it then use the binary package of g_mmpbsa. or
see here:

Pre-compiled executable program

Pre-compiled program does not require any external library or GROMACS and
APBS package. These programs are standalone and without any dependency.
Download, extract and use it.


http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html
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Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

[neha chaudhary]

Hello,

I have not installed APBS. I have compiled g_mmpbsa without APBS. Should I
compile it with APBS?

Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Aug 30, 2017 at 10:23 AM, Nikhil Maroli  wrote:

> Hi,
>
> The segmentation fault error during polar energy calculations is due to
> APBS. I don't know whether you installed it properly or not.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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>
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Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

[Nikhil Maroli]

Hi,

The segmentation fault error during polar energy calculations is due to
APBS. I don't know whether you installed it properly or not.
-- 
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