[gmx-users] Potassium ions in OPLS-AA

Lieven Buts lieven at ultr.vub.ac.be
Wed Jun 18 13:51:01 CEST 2003

When I tried to pdb2gmx a protein with a bound
potassium (K+) ion, defined in the PDB file as

ATOM   1033  K   K     133      16.212  -3.132  33.957  1.00 30.23

using the OPLS-AA force field (Gromacs 3.1.4),
I got the error message

                               :-)  pdb2gmx  (-:


Select the Force Field:
 0: Gromacs Forcefield (see manual)
 1: Gromacs Forcefield with all hydrogens (proteins only)
 2: GROMOS96 43a1 Forcefield (official distribution)
 3: GROMOS96 43b1 Vacuum Forcefield (official distribution)
 4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
Using ffoplsaa force field
Opening library file /usr/local/share/gromacs/top/ffoplsaa.atp
Atomtype 696
Reading residue database... (ffoplsaa)
Opening library file /usr/local/share/gromacs/top/ffoplsaa.rtp
Residue 50
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffoplsaa.hdb
Opening library file /usr/local/share/gromacs/top/ffoplsaa-n.tdb
Opening library file


5 out of 5 lines of specbond.dat converted succesfully
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Fatal error: Residue 'K' not found in residue topology database

When I use sodium instead (

ATOM   1033  NA  NA    133      16.212  -3.132  33.957  1.00 30.23

) everything works fine.

I looked at ffoplsaa.rtp, but it seems as if residue [ K ] is
properly defined.

Any ideas?

Lieven Buts
Brussels Free University

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