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

[Quyen V. Vu]

It's obvious from the error that you did not specify the position restraint
coordinates file while the define directive in mdp says using restraint.
As grompp suggestion:   gmx grompp -f nvt.mdp -c em.gro *-r em.gro* -p
topol.top -o nvt.tpr


On Fri, Jan 3, 2020 at 6:47 PM Navneet Kumar <navneetcdl at gmail.com> wrote:

> 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
> -------------------------------------------------------
>
>
>
>
>
>
> --
>
>
>
>
>
>
>      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)
> P +918017967647  <+918017967647> |
> E navneetcdl at gmail.com  <navneetcdl at gmail.com>
> <http://www.linkedin.com/in/navneet-kumar-74391814a/>
> <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>
>
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