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

Justin Lemkul jalemkul at vt.edu
Wed Nov 8 12:53:40 CET 2017

On 11/8/17 5:32 AM, Hermann, Johannes wrote:
> 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 = h-bonds).
> I hope this helps and can be adapted in the next version of charmm ff.

We'll get it fixed; it's a typo in the original CHARMM files (it's not 
the CGenFF file) that likely no one has ever noticed.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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