I gave the command gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr while doing the MD run in gromacs but I got the above error .But now I am in dilemma where the mistake is occuring in correcting the file name. I am confused plz help me out.I am attaching the files below.
Thanks
Amanpreet Kaur Take a look:
1. https://www.researchgate.net/post/Can_anyone_help_me_with_the_following_fault_in_Gromacs_during_the_NPT_equilibrium
2. https://www.researchgate.net/post/Fatal_error_Group_SOLV_referenced_in_the_mdp_file_was_not_found_in_the_index_file_Help_with_SLURM_HPC
3. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-October/075547.html
4. https://gromacs.org-gmx-users.maillist.sys.kth.narkive.com/14L9AFXQ/gmx-users-group-protein-lig-referenced-in-the-mdp-file-was-not-found-in-the-index-file-protein
Dear Amanpreet Kaur
As the error tells you, you are referencing to the group "Protein_benz" in your .mdp file but there is no Protein_benz group in the index file.
However, in the .mdp file you attach there is no reference to the Protein_benz group. Are you sure you are using the one you attached?
yes i am working in the same directory only. I think I have to edit somewhere according to the error .But where the editing should take place whether to rename a file or I Have to open some file and edit the name some where.
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