[gmx-users] Amide hydrogen naming in charmm 36 forcefield

[Justin Lemkul]

On 7/20/19 1:05 AM, Dilip.H.N wrote:
> Sir,
> I have also tried with atom name H, (i have checked in the .rtp file and is
> named as 'H'), but still i am getting the same following error:
>
> Atom HN in residue NMA 1 was not found in rtp entry NMA with 12 atoms
> while sorting atoms.
> First, i tried with naming the amide hydrogens as 'H' and got the
> above-mentioned error and then i followed the link
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-May/088942.html
> which
> stated "CHARMM has unique nomenclature for amide H atoms, so H needs to be
> renamed HN, though unfortunately, that's also wrong in the .rtp file. I'll
> fix that for the future." and hence i changed the 'H' into 'HN'.
>
> In spite in both the cases (naming the amide hydrogens as 'H' or 'HN'), i
> am getting the errors.

Probably the force field .arn file is responsible for this problem, by 
renaming all H to HN, which is actually incorrect for NMA.

> The amide nitrogens are not defined in the .hdb files in charmm36 FF too.

We have to write the .hdb entries by hand so we only create the ones we 
find useful. If you want to write one and verify it works, I can include 
it in a future version.

-Justin

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Justin A. Lemkul, Ph.D.
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