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

[Dilip.H.N]

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.

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

Any suggestions...?
Thank you.
---
With Best Regards,

Dilip.H.N
Ph.D. Student.


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20/07/19,
10:34:20

On Sat, Jul 20, 2019 at 5:30 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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