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

[Dilip.H.N]

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?

How can i solve this problem?

Any suggestions are appreciated.
Thank you.
---
With Best Regards,

Dilip.H.N
Ph.D. Student.


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19/07/19,
18:49:04