[gmx-users] Position restrain and other error while doing simulation

[Navneet Kumar]

Hello Everyone!


I am trying to simulate a system having a small protein and 10 small
molecules randomly distributed in box. I prepared the system using the
PACKMOL.

I am using the GROMACS 2018.4 and using "GROMOS96 54a7 force field.
Prepared the ligand topology ATB server.
Everything went fine till the addition of counter ions to neutralize the
system.
Aim of simulation is to study the interaction of protein and ligand.

Since small molecules are randomly distributed in box do I need to do these
steps
-Applying restrain to ligands
-Treatment of temperature coupling groups.

How to deal with this error.

Command line:
  gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr

Ignoring obsolete mdp entry 'title'
Setting the LD random seed to -685300895
Generated 210 of the 2556 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'OMSD'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...
Setting gen_seed to -369358517
Velocities were taken from a Maxwell distribution at 310 K
Removing all charge groups because cutoff-scheme=Verlet

-------------------------------------------------------
Program:     gmx grompp, version 2018.4
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
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     Thanks & Regards
_______________________________________________________

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
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E navneetcdl at gmail.com  <navneetcdl at gmail.com>
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