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

[João Henriques]

Hi Johannes,

I'd suggest contacting someone at the MacKerell Lab instead. I believe they
are responsible for the FF and for its maintenance. Otherwise this issue
might get lost here and never make it to the people that absolutely need to
know about it.

Look at the original paper and send an email to the corresponding authors:
http://www.nature.com/nmeth/journal/v14/n1/full/nmeth.4067.html

Cheers,
J

On Wed, Nov 8, 2017 at 11:32 AM, Hermann, Johannes <
J.Hermann at lrz.tu-muenchen.de> 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.
>
> All the best
>
> Johannes
>
> --
> ______________________________________
> *Technische Universität München*
> *Johannes Hermann, M.Sc.*
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