Adam Fraser wrote:
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.
If you don't supply an index file, grompp has some pre-defined groups.
I'm guessing they're case sensitive, though, so you should be using
"Protein", etc.
So I built an .ndx file with make_ndx and passed it to grompp with -n
and it still doesn't work.
Not very helpful. "Doesn't work" embraces a myriad of possibilities.
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"
See http://wiki.gromacs.org/index.php/topology_file
// 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?
Mark
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