[gmx-users] Problem in atom typing for Nitro group using CHARMM27

Archana Sonawani ask.archana at gmail.com
Thu Sep 20 10:39:11 CEST 2012

Dear Gromacs users,

I have simulated a protein-ligand complex. The ligand itp file was
generated using swissparam and it was further manually edited using the
atom types of charmm27 forcefield. But I found that the atom type for NO2
(nitro group) is not present in CHARMM27 forcefield.

*swissparam output*

51 NC=C 1 C50 N51 51 0.836 14.0067
52 O2CM 1 C50 O52 52 -0.468 15.9994
53 O2CM 1 C50 O53 53 -0.468 15.9994

*manually assigned groups for NO2 (using Accelrys DS CHARMM27 forcefield)*

51 NR3 1 C50 N51 51 0.836 14.0067    (charged histidine nitrogen)
52 O 1 C50 O52 52 -0.468 15.9994    (carbonyl oxygen)
53 O 1 C50 O53 53 -0.468 15.9994    (carbonyl oxygen)

After simulation, I visualized the pdb file and found the NO2 group was
seen as N(OH)2

Can anyone suggest what atomtype should be assigned for NO2 group while
using CHARMM27 forcefield ?

Thank you in advance.

Archana Sonawani-Jagtap
Junior Research Fellow,
Biomedical Informatics Centre,
Mumbai, India.

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