[gmx-users] Error while configuring gmx-3.3.1
padmanisandhu09 at gmail.com
Thu Aug 20 05:51:53 CEST 2015
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
On Wed, Aug 19, 2015 at 5:42 PM, Padmani Sandhu <padmanisandhu09 at gmail.com>
> 1. I am using it with CPMD as they have mentioned this version of gromacs
> 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.
> 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
>>> following commands:
>> Any reason you're using wildly outdated software?
>>> 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 >
>>> 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
>>> configure: creating ./config.status
>>> config.status: creating Makefile
>>> config.status: WARNING: Makefile.in seems to ignore the --datarootdir
>>> config.status: creating src/Makefile
>>> config.status: WARNING: src/Makefile.in seems to ignore the
>> This is not related.
>> 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
>> Gromacs Users mailing list
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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*
*Center for Computational Biology and Bioinformatics,*
*Central University of Himachal Pradesh,*
*Temporary Academic Block, Shahpur *
*Pin 176206, District Kangra,*
*Himachal Pradesh, India*
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