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 <[email protected]> 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 [email protected] <[email protected]> > <http://www.linkedin.com/in/navneet-kumar-74391814a/> > <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar> > > Please consider your environmental responsibility. Before printing this > e-mail message, ask yourself whether you really need a hard copy. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
