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

[Sailesh Bataju]

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.

Thank you for your time and effort.

Sailesh Bataju.