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

[rainy908 at yahoo.com]

Hi Justin,

I did not mention that I am indeed trying run Gromacs implementing the
MARTINI force field.  I realize this is not as automatic as selecting other
force fields in Gromacs using pdb2gmx.  This issue has been previously
discussed in:

http://www.mail-archive.com/gmx-users@gromacs.org/msg14945.html

-Lili

On 25 March 2010 18:13, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>
>>
> --
> ========================================
>
> 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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