[gmx-users] Typo for atom in charmm36-jul2017 ff for residue NAI

Hermann, Johannes J.Hermann at lrz.tu-muenchen.de
Wed Nov 8 11:33:01 CET 2017

Dear all,

I do not know if this is right place to put this, please feel free to 
redirect my comment.

I think I found a small typo in charmm36-jul2017 ff in the merged.rtp 
file for residue NAI:

In the [ atoms ] section line

N71N   HN1    0.260 69

should read

H71N   HN1    0.260 69

and consequently "N71N" should be replaced by "H71N" in the [ bonds ] 
and [ impropers ] sections. When you look at the structure, the 
H71N/N71N atom should clearly by an hydrogen atom. This can also be seen 
in the CHARMM-formatted topology and parameter files (in 
top_all36_cgenff.rtf, RESI NADH, the respective atom it is called NH71). 
If you leave N71N as it is, and rename H71N in your .gro/.pdb file, 
Gromacs will not treat the bond as hydrogen-bond (e.g. in constraints = 

I hope this helps and can be adapted in the next version of charmm ff.

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

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