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I am trying to perform MD simulations using CHARMM27 force field via GROMACS 2021.4.
The input structure file is a .pdb built from sequence using AmberTools20+tleap. The structure is c-terminated with NH2 and, by default, the "amino acid" is named as NHE (see last 5 lines of .pdb below).
When I attempt to generate GROMACS-required files for simulation, "NHE" residue is not found in the CHARM22 force field residue database.
What is the appropriated residue name for amide in CHARMM?

I tried changing residue name to "NH2", the obvious answer, and got no results. I checked the aminoacids* files, and found no solution.
There might be a simple answer I am missing or not understanding. Please let me know if there is a solution.

""""
ATOM 138 N NHE 11 24.340 34.120 25.340 1.00 0.00
ATOM 139 H1 NHE 11 24.450 34.930 25.930 1.00 0.00
ATOM 140 H2 NHE 11 23.460 33.920 24.870 1.00 0.00
TER
ENDMDL
""""

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rmv Online Content
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Peptide termini are typically handled as patches in the CHARMM force fields, rather than separate residues. The CHARMM27 force is deprecated, and has been supplanted by the CHARMM36 force field a number of years ago. Using the newer force field is recommended if you intend to publish the results.

This seems like more of a GROMACS question, which is outside the scope of these forums.

BTW, there is a forum here specifically for force field questions; this particular forum is for basic CHARMM usage questions. Did you not look at the READ BEFORE POSTING topic?


Rick Venable
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Thank you.

I read the March 2016 edited version, but failed to figure out the appropriate place for the post. Sorry about that.


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