[gmx-users] Error while configuring gmx-3.3.1
Padmani Sandhu
padmanisandhu09 at gmail.com
Thu Aug 20 14:32:15 CEST 2015
Thanks Mark, It worked. grompp working fine now.
regards,
Padmani
On Thu, Aug 20, 2015 at 4:14 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> 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 Any reason you're using wildly outdated software?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
> >
> > * 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-request at gromacs.org.
> >
> --
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>
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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*
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