[gmx-users] Error: No such moleculetype Protein

[Anirban Ghosh]

Hi,

I have worked around the problem. I was not including a .itp file. But now I
am getting Segmentation Fault:

Excluding 1 bonded neighbours for DSPC 104
Excluding 1 bonded neighbours for W 1397
Excluding 1 bonded neighbours for NA+ 0
Excluding 1 bonded neighbours for CL- 4

Number of fg atoms 410288
Number of cg atoms 57296
Reading frames from gro file 'Protein in DSPC Bilayer', 57296 atoms.
Reading frame       0 time    0.000   1297343010
Segmentation fault


Why is this happening?


Thanks,

Anirban


On Thu, Feb 10, 2011 at 5:45 PM, Anirban Ghosh <
reach.anirban.ghosh at gmail.com> wrote:

> 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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