[gmx-users] CHARMM36 in Gromacs :DNA terminus residues

Mehdi Bagherpour mehdi.bpour at gmail.com
Thu Jun 20 20:10:24 CEST 2019

Dear all,

I am trying to do MD simulation on my protein-DNA system in *Gromacs* using
*CHARMM36*  force field (*2019 version*, downloaded from Mackerell web

The DNA residue names start from DG5 ==> DC3 (in both DNA strand):

Once I do *pdb2gmx* command, seems it does not correctly recognize DNA
terminal residues (as defined by Justin Lemkul in .tdb files as 5TER and
3TER flags) and seems it treats DNA as a protein and hence I get this error:
*======== *

Start terminus *DG5*-1: *NH3+*
End terminus *DC3*-21: *COO-*

Program:     gmx pdb2gmx, version 2018.4
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1127)

Fatal error:
atom N not found in buiding block 1DG5 while combining tdb and rtp


Unfortunately, I was not able to fix this error and therefore I will
appreciate if someone could let me know how can I fix this problem.


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