Hello, I'm trying to get started working with a system of 2 hexadecane molecules in water but I'm having some trouble.
I'm getting the following error when I run: grompp -f simulate.mdp -c 2Hex_solv.gro -p 2Hex.top -o md.tpr Program grompp, VERSION 3.3.2 Source code file: readir.c, line: 794 Fatal error: Group protein not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. So I built an .ndx file with make_ndx and passed it to grompp with -n and it still doesn't work. Up until this point I've done the following: // convert pdb to gro editconf -f 2Hex.pdb -o 2Hex.gro // create topology file from .gro x2top -f 2Hex.gro -o 2Hex.top // build hexadecane.itp and include it in HexA.top (seems unneccessary) #include "hexadecane.itp" // create md input grompp -f minim.mdp -c 2Hex.gro -p 2Hex.top -o input.tpr // minimize structure mdrun -v -s input.tpr -o 2Hex_min.trr -c 2Hex_min.gro // set up box editconf -f 2Hex_min.gro -o 2Hex_min_box.gro -d 0.75 -bt cubic // solvate genbox -cp 2Hex_min_box.gro -cs spc216.gro -o 2Hex_solv.gro -p HexA.top #include "spc.itp" (in HexA.top) // finally attempting to build md input file grompp -f simulate.mdp -c 2Hex_solv.gro -p 2Hex.top -o md.tpr Any ideas what I might be doing wrong? Thanks much, Adam
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