[gmx-users] problem of sodium topology

Justin Lemkul jalemkul at vt.edu
Sun May 4 15:02:00 CEST 2014

On 5/4/14, 4:22 AM, Albert wrote:
> Hello:
> I am trying to generate topology for sodium ions under latest CHARMM36 FF with
> command:
> pdb2gmx -f na.pdb -o gmx.pdb
> here is the coordinate of my PDB file:
> HETATM 3425  NA  NA  A1220       0.643  -2.136  -1.619  1.00 26.62
> but it failed with messages:
> arning: Starting residue NA1220 in chain not identified as Protein/RNA/DNA.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
> 8 out of 8 lines of specbond.dat converted successfully
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.6.5
> Source code file: /home/albert/gromacs-4.6.5/src/kernel/resall.c, line: 642
> Fatal error:
> Residue 'NA' not found in residue topology database

Sodium ions are called "SOD" in CHARMM36, not "NA."  I don't really understand 
why you need pdb2gmx at all, though.  The topology is as simple as:

#include "charmm36.ff/forcefield.itp"
#include "charmm36.ff/ions.itp"
#include "charmm36.ff/tip3p.itp"

and then define the appropriate [molecules]



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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