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

Justin Lemkul jalemkul at vt.edu
Fri Jun 21 16:10:42 CEST 2019

On 6/20/19 4:58 PM, Mahdi Bagherpoor wrote:
> 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
> homepage).
> 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.

You have to manually choose termini with CHARMM36. This is because there 
is no way to split proteins, nucleic acids, etc. into their own files 
automatically when reading in the whole force field and we try to avoid 
hard-coding as much as we possibly can.


> Cheers,
> Mahdi


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


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