[gmx-users] force field / parameters for NADH, FMN

Hermann, Johannes J.Hermann at lrz.tu-muenchen.de
Mon Oct 30 15:58:35 CET 2017

Dear all,

I want to simulate a complex consisting of a protein, FMN, and NADH. I 
have two problems/questions:

1) In the "CHARMM36 all-atom force field (March 2017)" parameters for 
NADH are present. But apparently I am using a wrong atom naming 
convention (I copied / pasted NADH from a pdb entry):

Fatal error:
Atom PN in residue NADH 0 was not found in rtp entry NADH with 71 atoms
while sorting atoms.

How can I generate a appropriate input file for gromacs gmx2pdb?

2) I did not find FMN in the charmm36 force field. Can some recommend me 
a program to generate a parameter file? And how to proceed with it?

Thank you all in advance!

All the best


*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.hermann at lrz.tum.de

More information about the gromacs.org_gmx-users mailing list