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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