[gmx-users] grompp: no such moleculetype
Francesco Pietra
francesco.pietra at accademialucchese.it
Mon Oct 5 20:15:36 CEST 2009
On Mon, Oct 5, 2009 at 7:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Francesco Pietra wrote:
>>
>> On Mon, Oct 5, 2009 at 4:39 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>
>>> Francesco Pietra wrote:
>>>>
>>>> Thanks, and beg pardon for the pedestrian mistake.
>>>>
>>>> However, I am not yet out. .tpr not generated
>>>>
>>>> With command
>>>>
>>>> $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -o
>>>> mod21.cg.tpr
>>>>
>>>>
>>>> There are: 0 OTHER residues
>>>> There are: 1270 PROTEIN residues
>>>> There are: 0 DNA residues
>>>> Analysing Protein...
>>>>
>>>> -------------------------------------------------------
>>>> Program grompp, VERSION 3.3.3
>>>> Source code file: ../../../../src/kernel/readir.c, line: 798
>>>>
>>>> Fatal error:
>>>> Group DPPC not found in indexfile.
>>>> Maybe you have non-default groups in your mdp file, while not using
>>>> the '-n' option of grompp.
>>>> In that case use the '-n' option.
>>>>
>>>> As I said before, I am using the mdp file as provided by MARTINI.
>>>> ============
>>>>
>>> Then you haven't yet appropriately #included the .itp file for DPPC.
>>
>> As I said, I don't understand why about DPPC. The protein is pure
>> standard amino acids and nothing else. I am trying to get the files
>> for simulation in vacuum. I have reexamined all the stuff and I don't
>> see any allusion to a bilayer, unless that comes from the .mdp file.
>> The .top I used in these last attempts reads:
>
> I would suggest looking at the .mdp file; grompp wouldn't be complaining if
> there wasn't some input file specifying an unknown molecule.
I have now used protein-in-vacuum.mdp from the ubiquitin cg tutorial.
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.
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.
Hope to be able to come again here with a solution of this affair.
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
>>>>>
>>>>> ========================================
>>>>> _______________________________________________
>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>> 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
>>>
>>> ========================================
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
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>>> Please search the archive at http://www.gromacs.org/search before
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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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> Please search the archive at http://www.gromacs.org/search before posting!
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