[gmx-users] MD with DNA double strand

Amali Guruge amaligg2010 at gmail.com
Thu Sep 17 08:03:41 CEST 2015

Dear Gromacs users,

I want to do a molecular dynamic simulation for my enzyme-ligand complex.
The enzyme is topoisomerase I. I used the pdb id 1K4T for the simulation
and I need to keep the DNA double strand with the enzyme.

I replaced the 5'-sulfhydryl group into a 5'-hydroxyl group before starting
the simulation.

I gave the command 'pdb2gmx -f receptor.pdb -inter -p system.top -o
recep01.pdb -ignh'. I selected AMBER99 as the force field while SPC/E was
used as the water model.
Then I got the following error.

Fatal error:
Atom O in residue DG 11 was not found in rtp entry DG with 33 atoms
while sorting atoms.

How can I solve this problem? Can anyone help me?

Thank you.

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