Dear GROMACS users I received the following error while running grompp to prepare the .tpr file before the initial energy minimization of my system.
*Fatal error:Group DNA_chain_D referenced in the .mdp file was not found in the index file.Group names must match either [moleculetype] names or custom index groupnames, in which case you must supply an index file to the '-n' optionof grompp.* I used the following few commands in succession before this :- (1) pdb2gmx -f 1HAO.pdb -o complex.gro -p complex.top (2) editconf -f complex.gro -o complex_box.gro -bt dodecahedron -d 1.0 (3) genbox -cp complex_box.gro -cs spc216.gro -p complex.top -o complex_solv.gro (4) grompp -f em.mdp -c complex_solv.gro -p complex.top -o ions.tpr (5) genion -s ions.tpr -o complex_ions.gro -p complex.top -pname NA -nname CL -neutral -conc 0.1 (6) grompp -f em_real.mdp -c complex_ions.gro -p complex.top -o em.tpr After command (6) error is coming. In em.mdp file , at step (4) I have , "energygrps = system" and in em_real.mdp file at step (6) I have ," nenergygrps = DNA_chain_D Protein_chain_L Protein_chain_H . ( Note : These files I gathered from Dr. Lemkuls tutorial on protein-ligand system ) Also my complex.top file has the following :- ; Include chain topologies #include "complex_DNA_chain_D.itp" #include "complex_Protein_chain_L.itp" #include "complex_Protein_chain_H.itp" ........................................................... ........................................................... [ molecules ] ; Compound #mols DNA_chain_D 1 Protein_chain_L 1 Protein_chain_H 1 SOL 13578 NA 39 CL 28 and , "complex_DNA_chain_D.itp" has the following :- [ moleculetype ] ; Name nrexcl DNA_chain_D 3 Similar statements are available in the other two .itp files mentioned in the complex.top file. Now I am unable to understand what the error statement means by specifying "index file" ?? Please shed some light upon this. I have also consulted the error section of the GROMACS documentation but could not understand. Thanks & Regards, Agnivo Gosai Grad. Student , Iowa State University -- 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 gmx-users-requ...@gromacs.org.