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

[Justin A. Lemkul]

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.

-Justin

> Thanks in advance,
> Lili
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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