[gmx-users] SwissParam and Gromacs

Amali Guruge amaligg2010 at gmail.com
Fri Dec 4 10:18:20 CET 2015

Dear All,

I submitted docked conformation of topotecan molecule to the SwissParam
server and I got itp file. Then I did a molecular dynamic simulation using
that itp file (I used Gromacs software with CHARMM27 force field)

When I tried to run the command,
 grompp -c b4em.pdb -f em01.mdp -n index.ndx -p system.top -o em01.tpr

it gave the following error.

*Fatal error:Atomtype CB not found*
I attached the itp file received from the server. Please help me to correct
this error.

Thank you.

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