[gmx-users] Error while configuring gmx-3.3.1
padmanisandhu09 at gmail.com
Wed Aug 19 14:12:36 CEST 2015
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 using
>> 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 Any reason you're using wildly outdated software?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 --datarootdir
> 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
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