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

[rainy908 at yahoo.com]

Yup.  Initially I was just confused on how to parameterize the protein using
the MARTINI ff.  I thought there was an automatic way to do it using pdb2gmx
only to see Gromos force fields available.  But now I realize I have to
generate the .itp file using the perl script.  Anyway, I've got it figured
out :).  Thanks for your concern though.

On 25 March 2010 19:22, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> rainy908 at yahoo.com wrote:
>
>> 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
>>
>>
> Did you follow the actual tutorial on the MARTINI site?  You should not
> ever have to invoke pdb2gmx.  Topology generation is conducted using
> MARTINI-specific scripts.  In the future, it will save a lot of time (both
> yours and ours) if you provide complete, legitimate information.  After all,
> you do not want to use Gromos96, but your first post clearly stated that you
> were trying to use this force field.  If you want free help, make it easy
> for us to do so.
>
> -Justin
>
>  -Lili
>>
>> On 25 March 2010 18:13, Justin A. Lemkul <jalemkul at vt.edu <mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>
>>    rainy908 at yahoo.com <mailto: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 <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
>>
>>
>>
>>
>>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100325/9b58927a/attachment.html>