[gmx-users] Error while configuring gmx-3.3.1

[Mark Abraham]

Hi,

Apparently the 3.3.1 install isn't working well for you. You can use cp -R
gromacs-3.3.1/share/top/* /usr/local/gromacs/share/top/ which is a standard
unix command.

Mark

On Thu, Aug 20, 2015 at 5:52 AM Padmani Sandhu <padmanisandhu09 at gmail.com>
wrote:

> 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 Any reason you're using wildly outdated software?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
> >>
> >> ==================================================
> >> --
> >> 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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> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >
> >
> >
> > --
> > *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*
> --
> Gromacs Users mailing list
>
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