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

[neha chaudhary]

Dear Sir/Ma'am,

I am trying to run g_mmpbsa for gromacs-5.1.2. It is working fine for MM
energy and apolar energy but when I am trying to run this for polar energy,
g_mmpbsa run is stopping giving error: Segmentation fault (core dumped).

Previously I was using gromacs 4.6 with same g_mmpbsa version, then it was
working fine. Now I installed g_mmpbsa from source code for 5.1.2 but it is
not working though it installed properly without any errors.

Please help me with the issue.

Best Regards,

Neha
-- 
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.

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

[Nikhil Maroli]

Hi, Install  Pre-compiled executable program
You might wrongly be compiled for :
Includes APBS functionality

use with
To use with external APBS program
-- 
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.

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

[neha chaudhary]

Thank you for replying,

 I have compiled g_mmpbsa without apna. I have tried with pre-compiled
binary as well but no success.

On 29-Aug-2017 3:45 PM, "Nikhil Maroli"  wrote:

> [image: Boxbe]  This message is eligible
> for Automatic Cleanup! (scinik...@gmail.com) Add cleanup rule
> 
> | More info
> 
>
> Hi, Install  Pre-compiled executable program
> You might wrongly be compiled for :
> Includes APBS functionality
>
> use with
> To use with external APBS program
> --
> 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.
>
>
-- 
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.

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.
-- 
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.

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!
>
> * 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.
>
-- 
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.

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
-- 
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.

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.
>
-- 
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.

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.
>>
>
>
-- 
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.