[gmx-users] Fatal error: Atomtype Qd not found

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 26 02:13:06 CET 2010

rainy908 at yahoo.com wrote:
> Dear GMX users,
> I have a quick question regarding which Gromacs force field in pdb2gmx 
> is best suited for creating a topology (itp) file for the enzyme, 
> lactate oxidase.  So far the force fields in Gromacs 4.0.4 are:
>  0: GROMOS96 43a1 force field
>  1: GROMOS96 43a2 force field (improved alkane dihedrals)
>  2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>  3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>  4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>  5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>  6: [DEPRECATED] Gromacs force field (see manual)
>  7: [DEPRECATED] Gromacs force field with hydrogens for NMR
>  8: Encad all-atom force field, using scaled-down vacuum charges
>  9: Encad all-atom force field, using full solvent charges  
> I selected the "G53a6 GROMOS96 53a6 Forcefield" for creating my itp 
> file, however, when I try to run grompp to generate the .tpr file, I get 
> the error:
> -------------------------------------------------------
> Program grompp_d, VERSION 4.0.4
> Source code file: toppush.c, line: 947
> Fatal error:
> Atomtype Qd not found
> -------------------------------------------------------
> I've looked into other discussions on this 
> (http://www.mail-archive.com/gmx-users@gromacs.org/msg15722.html), and 
> concluded that the atomtype Qd must not be present in the G53a6 force 
> field.  My system is simply the protein lactate oxidase.  Does anyone 
> have suggestions on which force field(s) is best suited for this molecule?

Since the atom type "Qd" is not present in the 53a6 parameter set, this error 
has nothing to do with the appropriateness of your force field choice. 
Somewhere, you've incorporated a nonsensical atom type.  The only time I have 
ever seen "Qd" is in the MARTINI coarse grain force fields.  Be sure you're 
using the topologies you think you are; if you really are using an unaltered 
pdb2gmx-generated topology for 53a6, there is no way that this atom type would 
be found therein.


> Thanks in advance,
> Lili


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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