Hello,<br><br>I'm trying to get started working with a system of 2 hexadecane molecules in water but I'm having some trouble.<br><br>I'm getting the following error when I run: <br> grompp -f simulate.mdp -c 2Hex_solv.gro -p
2Hex.top -o md.tpr<br><br><div style="margin-left: 40px;">Program grompp, VERSION 3.3.2<br>Source code file: readir.c, line: 794<br><br>Fatal error:<br>Group protein not found in indexfile.<br>Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.
<br>In that case use the '-n' option.<br></div><br>So I built an .ndx file with make_ndx and passed it to grompp with -n and it still doesn't work.<br><br>Up until this point I've done the following:<br><br>
<div style="margin-left: 40px;"><span style="font-weight: bold;">// convert pdb to gro</span><br>editconf -f 2Hex.pdb -o 2Hex.gro<br><br><span style="font-weight: bold;">// create topology file from .gro</span><br>x2top -f
2Hex.gro -o 2Hex.top<br><br><span style="font-weight: bold;"> // build hexadecane.itp and include it in HexA.top (seems unneccessary)</span><br> #include "hexadecane.itp" <br><br><span style="font-weight: bold;">
// create md input</span><br>grompp -f minim.mdp -c 2Hex.gro -p 2Hex.top -o input.tpr<br><br><span style="font-weight: bold;">// minimize structure</span><br>mdrun -v -s input.tpr -o 2Hex_min.trr -c 2Hex_min.gro<br><br><span style="font-weight: bold;">
// set up box </span><br>editconf -f 2Hex_min.gro -o 2Hex_min_box.gro -d 0.75 -bt cubic<br><br><span style="font-weight: bold;">// solvate</span><br>genbox -cp 2Hex_min_box.gro -cs spc216.gro -o 2Hex_solv.gro -p HexA.top<br>
<br><span style="font-weight: bold;"></span> #include "spc.itp" (in HexA.top)<br><br><span style="font-weight: bold;">// finally attempting to build md input file</span><br>grompp -f simulate.mdp -c 2Hex_solv.gro -p
2Hex.top -o md.tpr<br></div><br><br>Any ideas what I might be doing wrong?<br><br>Thanks much,<br>Adam<br><br>