Dear Gromacs users,<br>I have a problem in simulating microtubule hetero-dimer. I was trying to include K+ and CL- ions to counter balance as well as to maintain the desired concn (intra cellular concentration of KCl is approx 140mM) using the command <br>
genion -s ions.tpr -o solv_ions.gro -p topol.top -pname K -nname CL -conc 0.14 -neutral <br>But I got an error like "<b>Molecule type K is not found</b>" (gromos43a1ff). Even after the inclusion of K+ ion topology in gromos43a1ff/ions.itp, I got the same error. Next time I have changed the forcefield to <b>Amber99sb-ildn</b>. But this time it has given some different error like <b>atom type NR is not found </b>(I suppose this is due to the ligand topology generated by PRODRG). Please help me in this regard.<br>
<br>Thanking you <br clear="all"><br><br>With Best Wishes<br>Venkat Reddy Chirasani<br>IITM<br>