[gmx-users] grompp: no such moleculetype

Mon Oct 5 20:20:44 CEST 2009

Francesco Pietra wrote:

> I have now used protein-in-vacuum.mdp from the ubiquitin cg tutorial.

Which tutorial is that?  Can you provide a link?

> Again grompp complains that "Fatal error:
> Group Non-Protein not found in indexfile. Maybe you have non-default
> goups in your mdp file, while not using the '-n' option of grompp. In
> that case use the '-n' option." (no more complaining about DPPC, now
> more generic non-protein, which increases the confusion)
> 
> Having ruled out the .mdp file as responsible for that, it was easy to
> check that both the protein.gro and the protein.itp files only specify
> standard amino acids.
> 

Why have you ruled the .mdp file out?  You will probably find the word 
"Non-Protein" somewhere in the .mdp file, most likely in T-coupling groups.  If 
you have a protein in vacuo, the only groups allowed for T-coupling would be 
Protein or System, unless you have specifically made some custom index groups 
(but you probably don't want to in this case).

Look at the .mdp file.  You will find Non-Protein somewhere.

> I'll settle the matter until I can generate ideas, or be less tired to
> check again for the presence of that mysterious non-protein. The real
> protein contains chloride ion ligands. I have cleared from them before
> starting with CG and anyway no trace of cl CL Cl.
> 

So that has nothing to do with it.

> Hope to be able to come again here with a solution of this affair.
> 

The best advice - don't blindly use some .mdp file you find because it works for 
a tutorial.  Read it, read the manual, and make changes based on what you 
actually have in your system.

-Justin

> thanks
> francesco
> PS: the protein CG file contains TER lines separating the subunits,
> but the CG .gro file has no TER.
> 
> 
>> -Justin
>>
>>> ;
>>> ; mod21 | MARTINI 2.1
>>> ;
>>>
>>> ; Include force field poarameters containing all particle definitions,
>>> ; the interaction matrix, plus the topology for water.
>>>
>>> #include "martini_v2.1.itp"
>>>
>>> ; Then include the file(s) containing the topologies of other
>>> ; molecules present in your system.
>>>
>>> ; #include "martini_v2.0_lipids.itp"
>>> ; #include "martini_v2.0_salt.itp"
>>>
>>>
>>> #include "mod21.itp"
>>>
>>> ; Define a name for your system
>>>
>>> [ system ]
>>> mod21
>>>
>>> ; Define the composition of your system
>>> ; The molecule names should correspond to those defined in the itp
>>> file(s).
>>>
>>> [ molecules ]
>>> Protein 1
>>> ; DPPC 128
>>> ; W 2000
>>> ; NA+ 20
>>> ; CL- 20
>>>
>>> It seems that commenting out ";" is placed correctly.
>>>
>>> I am sincerely sorry to bother you again.
>>>
>>> francesco
>>>
>>>
>>>
>>>>> With command
>>>>>
>>>>> $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -n
>>>>> -o mod21.cg.tpr
>>>>>
>>>>> NOTE:
>>>>>  System has non-zero total charge: -5.000000e+01
>>>>>
>>>>> processing coordinates...
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (BCQd - BN0)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (SCAC1 - SC1)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (BCP5 - BN0)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (SCP1 - SC1)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (BSP5 - BN0)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (SSAC1 - SC1)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (BCP5 - BN0)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (SCC3 - SC1)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (SCQd - SC2)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (BCP5 - BN0)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (SCN0 - SC1)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (SCQd - SC2)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (BHN0 - BN0)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (BHNd - BN0)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (SHAC1 - SC1)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (BHNd - BN0)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (SHSC4 - SC2)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (SHSP1 - SC1)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (SHSC4 - SC3)
>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match
>>>>> (SHSC4 - SC4)
>>>>> (more than 20 non-matching atom names)
>>>>> WARNING 2 [file "mod21.cg.top", line 28]:
>>>>>  2875 non-matching atom names
>>>>>  atom names from mod21.cg.top will be used
>>>>>  atom names from mod21.cg.box.gro will be ignored
>>>>>
>>>>> double-checking input for internal consistency...
>>>>> renumbering atomtypes...
>>>>> converting bonded parameters...
>>>>> #      BONDS:   2724
>>>>> #  G96ANGLES:   2860
>>>>> #      PDIHS:   328
>>>>> #      IDIHS:   187
>>>>> #     CONSTR:   745
>>>>> Walking down the molecule graph to make shake-blocks
>>>>> initialising group options...
>>>>> processing index file...
>>>>>
>>>>> -------------------------------------------------------
>>>>> Program grompp, VERSION 3.3.3
>>>>> Source code file: ../../../../src/gmxlib/futil.c, line: 345
>>>>>
>>>>> File input/output error:
>>>>> index.ndx
>>>>> ==========
>>>>> Non-matching because of the many -S-S- bonds? Why asking about
>>>>> index.ndx?
>>>>>
>>>> Non-matching names occur because MARTINI doesn't assign them correctly in
>>>> the initial system setup.  Using the .top names is fine.
>>>>
>>>> The I/O error comes from the fact that you have passed the -n flag to
>>>> grompp
>>>> without having index.ndx in the working directory.  Note that having an
>>>> index file doesn't necessarily solve your problem; the warning is printed
>>>> in
>>>> case you have non-default groups for, e.g., T-coupling or energygrps.  If
>>>> you have a "moleculetype not found," then you haven't #included the .itp
>>>> file and an index file won't save you.
>>>>
>>>> -Justin
>>>>
>>>>> Thanks for help
>>>>> francesco
>>>>>
>>>>>
>>>>> On Mon, Oct 5, 2009 at 12:33 PM, Justin A. Lemkul <jalemkul at vt.edu>
>>>>> wrote:
>>>>>> Francesco Pietra wrote:
>>>>>>> Hi:
>>>>>>>
>>>>>>> As I found it difficult to manage solvation - the way I would like -
>>>>>>> with a pore protein (a trimer) partly immersed into a bilayer, I
>>>>>>> started with the protein alone in vacuum, in order to try to fix the
>>>>>>> problems step-by-step. Unfortunately, I can't fix simple problems with
>>>>>>> grompp.
>>>>>>>
>>>>>>> 1) Generated mod21.itp from mod21.pdb
>>>>>>>
>>>>>>> 2) Generated mod21.cg.pdb with awk script)
>>>>>>>
>>>>>>> 3) editconf -f mod21.cg.pdb -o mod21.cg.gro
>>>>>>>
>>>>>>> 4) genbox -cp mod21.cg.gro -box 10 17 10 -o mod21.cg.box.gro
>>>>>>>
>>>>>>> 5) grompp -np 4 -f mod21.cg.box.mdp  -c mod21.cg.box.gro -p
>>>>>>> mod21.cg.box.top -warnmax 10
>>>>>>>
>>>>>>>  Error: no such moleculetype Protein.
>>>>>>>
>>>>>>> .............................
>>>>>>> .mdp is merely a renamed martini_v2.0.example.mdp, taking care that
>>>>>>> "cpp  = /usr/bin/cpp".
>>>>>>>
>>>>>>> .top was from editing martini_v2.0.example.top and reads (in between
>>>>>>> ===):
>>>>>>> ======
>>>>>>> ;
>>>>>>> ; mod21 | MARTINI 2.1
>>>>>>> ;
>>>>>>>
>>>>>>> ; Include force field parameters containing all particle definitions,
>>>>>>> ; the interaction matrix, plus the topology for water.
>>>>>>>
>>>>>>> #include "martini_v2.1.itp"
>>>>>>>
>>>>>>> ; Then include the file(s) containing the topologies of other
>>>>>>> ; molecules present in your system.
>>>>>>>
>>>>>>> ; #include "martini_v2.0_lipids.itp"
>>>>>>> ; #include "martini_v2.0_salt.itp"
>>>>>>>
>>>>>>> #include mod21.itp
>>>>>>>
>>>>>> This #include statement has the wrong syntax.  See any of the above for
>>>>>> the
>>>>>> correct way to do it.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>> --
>>>>>> ========================================
>>>>>>
>>>>>> Justin A. Lemkul
>>>>>> Ph.D. Candidate
>>>>>> ICTAS Doctoral Scholar
>>>>>> 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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>>>>>>
>>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> 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
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>>>> interface
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>>>>
>>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> 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!
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>>
>>
> 

-- 
========================================

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

========================================