<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hello</div><div><br></div><div>I took parameters that are calculated for a charmm22 forcefield and I want to use it with a charmm27 forcefield (I have the same molecule as the people who calculated the charmm22 parameters but they didn't use gromacs). I made a .rtp, .hdb and residuetypes.dat file and edit the atomtypes.atp file. pdb2gmx works well, also generating a box and use of SPC Water system. :-)</div><div><br></div><div>The problem starts with grompp. My command was: grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr</div><div><br></div><div>The Error is:<br></div><div><br></div><div>Program grompp, VERSION 4.5.5<br>Source code file: /home/me/src/gromacs-4.5.5/src/kernel/toppush.c, line: 1166<br><br>Fatal error:<br>Atomtype CN1B not found<br>For more information and tips for
troubleshooting, please check the GROMACS<br>website at http://www.gromacs.org/Documentation/Errors<br></div><div><br></div><div><br></div><div>I read in old mails here in the mailing list and found some similar problems but I don't understood it. Here is my question:</div><div><br></div><div>I know that grompp doesn't use the atomtypes.dat file in which I defined what CN1B is (only pdb2gmx needs it). Where exactly do I have to define my atomtypes for grommp? In a new .itp file, or in my .top file wich pdb2gmx created or in the forcefield files in charmm27 like ffbonded.itp and so on. <br></div><br>Thanks for help<br>Greetings<br>Lara<br><div><br></div><div></div></div></body></html>