[gmx-users] Error: No such moleculetype Protein

[Anirban Ghosh]

Hi Tsjerk,

Thanks for the reply.
Yes, I had a reference to 'Protein' group in my .mdp file while running the
CGMD. Now, after CG run I am trying to convert the CG to FG model using:

g_fg2cg -pfg topol_fg.top -pcg system_cg.top -n 0 -c cg.gro -o fg.gro

So do I need to supply any other parameter to this command or how to mention
this refering of 'Protein' group here.

Thanks,

Anirban



On Thu, Feb 10, 2011 at 5:28 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Anirban,
>
> Probably you have a reference to a group 'Protein' in your .mdp file.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh
> <reach.anirban.ghosh at gmail.com> wrote:
> > Hi,
> > I am trying to convert a CG system containing multiple copies of a
> protein +
> > lipid + water + ions to an all-atom system using the special
> gromacs_reverse
> > version command g_fg2cg. However I am getting the error:
> >
> -----------------------------------------------------------------------------------------------
> > calling cpp...
> > processing topology...
> > Generated 4 of the 780 non-bonded parameter combinations
> > Cleaning up temporary file grompp9YJMaA
> > -------------------------------------------------------
> > Program g_fg2cg, VERSION 3.3.1
> > Source code file: ../kernel/toppush.c, line: 1293
> > Fatal error:
> > No such moleculetype Protein
> >
> ---------------------------------------------------------------------------------------------
> > I have checked all the include statements and .itp files, but cannot fix
> the
> > issue. Is seems to be very trivial but still exists.
> > Any suggestion is welcome.
> >
> > Thanks,
> > Anirban
> > --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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