[gmx-users] Error while configuring gmx-3.3.1

[Padmani Sandhu]

1. I am using it with CPMD as they have mentioned this version of gromacs
only.
2. The top-level force fields are not included as they are not present in
/usr/local/gromacs/share/top/ file  for eg. BH4_oplsaa.itp, however its
there in the gmx-3.3.1_qmmm-1.3.2/share/top folder.
3. There is no problem with topology, its working fine with gromacs-4.5.6
and later versions.




Thanks


Padmani

On Wed, Aug 19, 2015 at 5:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/19/15 7:58 AM, Padmani Sandhu wrote:
>
>> Hello everyone,
>>
>> I am trying to install gmx-3.3.1 on ubuntu 14.04. I have compiled it using
>> following commands:
>>
>>
> Any reason you're using wildly outdated software?
>
> ./configure
>> make
>> sudo make install
>>
>> *However the program was installed but while running grommp, it was
>> terminated with  an error :*
>>
>> checking input for internal consistency...
>> calling cpp...
>> In file included from /usr/local/gromacs/share/top/ffoplsaa.itp:23:0,
>>                   from topol.top:11:
>> /usr/local/gromacs/share/top/ffoplsaabon.itp:2692:26: fatal error:
>> BH4_oplsaa.itp: No such file or directory
>>   #include "BH4_oplsaa.itp"
>>
>>               ^
>
>> compilation terminated.
>>
>
> You probably shouldn't be #including files in top-level force field files.
>
> cpp exit code: 256
>> Tried to execute: 'cpp  -I/usr/local/gromacs/share/top  topol.top >
>> gromppVUW784'
>> The 'cpp' command is defined in the .mdp file
>> processing topology...
>> processing coordinates...
>> -------------------------------------------------------
>> Program grompp, VERSION 3.3.1
>> Source code file: grompp.c, line: 448
>>
>> Fatal error:
>> number of coordinates in coordinate file (conf_solv.gro, 317253)
>>               does not match topology (topol.top, 0)
>>
>>
> Your topology is totally wrong or misformatted.
>
>
>> *I had an error while running ./configure that might be causing this
>> problem*
>>
>> configure: creating ./config.status
>> config.status: creating Makefile
>> config.status: WARNING:  Makefile.in seems to ignore the --datarootdir
>> setting
>> config.status: creating src/Makefile
>> config.status: WARNING:  src/Makefile.in seems to ignore the --datarootdir
>> setting
>>
>>
> This is not related.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
*Padmani sandhu*
*Research Scholar,*
*Center for Computational Biology and Bioinformatics,*
*Central University of Himachal Pradesh,*
*Temporary Academic Block, Shahpur *
*Pin 176206, District Kangra,*
*Himachal Pradesh, India*