[gmx-users] Error while configuring gmx-3.3.1

[Padmani Sandhu]

Hello Justin,


I have copied both the .itp files which were giving error in to
/usr/local/gromacs/share/top using command:

sudo cp BH4_oplsaa.itp /usr/local/gromacs/share/top

sudo cp ffoplsaabon.itp /usr/local/gromacs/share/top

and now grompp worked. Please can you suggest me any solution so that all
the files in *gromacs-3.3.1/share/top *can be copied to
*/usr/local/gromacs/share/top.*



Thanks


Padmani


On Wed, Aug 19, 2015 at 5:42 PM, Padmani Sandhu <padmanisandhu09 at gmail.com>
wrote:

> 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 Any reason you're using wildly outdated software?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*
>



-- 
*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*