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

[Navneet Kumar]

Do I need to  Applying restrain to ligands
-Treatment of temperature coupling groups as we do in protein ligand
complex bound to each other. But in my case ligands are randomly
distributed around protein. What should a mdp file look like in this case.
I am trying to simulate the beta amyloid with some Polyphenols to see
effect of these molecules on beta amyloid aggregation.

On Sat, 4 Jan 2020, 00:33 Quyen V. Vu, <vuqv.phys at gmail.com> wrote:

> 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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