[gmx-users] Error while configuring gmx-3.3.1

[Justin Lemkul]

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Any reason you're using wildly outdated software?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

==================================================