[gmx-users] Cannot find position restraint file restraint.gro

[Justin Lemkul]

On 1/22/18 2:20 AM, Sailesh Bataju wrote:
> Hi,
>
> I have been trying to simulate isobutane in urea as a solvent. I have made
> myself urea.itp and urea.gro file for charmm36 forcefield under
> equilibrating at certain temperature and pressure. First nvt followed by
> npt I got error like this while equilibriating.
>
> Program:     gmx grompp, version 2018
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008)
>
> Fatal error:
> Cannot find position restraint file restraint.gro (option -r).
>  From GROMACS-2018, you need to specify the position restraint coordinate
> files
> explicitly to avoid mistakes, although you can still use the same file as
> you
> specify for the -c option.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Despite of this error, I continue comment define= -DPOSRE in .mdp file.
> Then the simulation run smoothly without any error.
>
> After urea has been equilibriated in  a box under certain temperature and
> pressure . Now i've to put isobutane molecule in it. There has been no
> error till energy minimization. But when i've to equilibriate in nvt, I got
> error like this.
>
> GROMACS:      gmx grompp, version 2018
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Working dir:  /home/sailesh/Documents/Thesis/urea_1000
> Command line:
>    gmx grompp -f nvt_urea.mdp -c em_urea.gro -p topol.top -o nvt_urea.tpr
>
> Ignoring obsolete mdp entry 'title'
> Generated 85052 of the 85078 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 55198 of the 85078 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Alkane_chain_A'
> Excluding 3 bonded neighbours molecule type 'Urea'
> Velocities were taken from a Maxwell distribution at 298 K
> Removing all charge groups because cutoff-scheme=Verlet
>
> -------------------------------------------------------
> Program:     gmx grompp, version 2018
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008)
>
> Fatal error:
> Cannot find position restraint file restraint.gro (option -r).
>  From GROMACS-2018, you need to specify the position restraint coordinate
> files
> explicitly to avoid mistakes, although you can still use the same file as
> you
> specify for the -c option.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> turning all bonds into constraints...
> turning all bonds into constraints...
>
> This is my end part of topol.top file for isobutane in urea.
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include urea topology
> #include "charmm36.ff/urea.itp"
> #ifdef POSRES
> #include "posre_urea.itp"
> #endif
>
> ; Include topology for ions
> #include "charmm36.ff/ions.itp"
>
> [ system ]
> ; Name
> Isobutane in Urea
>
> [ molecules ]
> ; Compound        #mols
> Alkane_chain_A      2
> Urea 841­
>
> Any idea to solve this problem.

The error message tells you exactly what to do (it's probably one of the 
most verbose error messages I've ever seen). The -r argument is now 
required.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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