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

[Justin Lemkul]

On 7/19/19 9:26 AM, Dilip.H.N wrote:
> Hello,
> I tried to get the topology for the N-methyl acetamide (NMA) through gmx
> pdb2gmx command in charmm 36 FF,
> but the following error states:
>
> Atom HN in residue NMA 1 was not found in rtp entry NMA with 12 atoms
> while sorting atoms.
> For a hydrogen, this can be a different protonation state, or it
> might have had a different number in the PDB file and was rebuilt
> (it might for instance have been H3, and we only expected H1 & H2).
> Note that hydrogens might have been added to the entry for the N-terminus.
> Remove this hydrogen or choose a different protonation state to solve it.
> Option -ignh will ignore all hydrogens in the input.
>
> When searched i found the following link
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-May/088942.html
>
> which states that "CHARMM has unique nomenclature for amide H
> atoms,.........." as stated by Dr. Justin lemkul. Even in the .hdb file,
> the naming has not been addressed.
> I have tried renaming the amide hydrogen into 'HN' from 'H' but still gives
> the error.  Why is this amide hydrogen unnamed in Charmm 36 FF...?
>
> So, May i know has this issue been resolved?

The atom name is H. Check the NMA entry in the .rtp file and you will 
see this.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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