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

[Justin Lemkul]

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

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

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