[gmx-users] problem of sodium topology

Albert mailmd2011 at gmail.com
Sun May 4 10:23:01 CEST 2014

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

thank you very much

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