[gmx-users] Atomtype not found - grompp - charmm27 and charmm22

[Lara Bunte]

Hello

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.  :-)

The problem starts with grompp. My command was: grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr

The Error is:


Program grompp, VERSION 4.5.5
Source code file: /home/me/src/gromacs-4.5.5/src/kernel/toppush.c, line: 1166

Fatal error:
Atomtype CN1B not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



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:

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. 

Thanks for help
Greetings
Lara
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