[gmx-users] grompp: no such moleculetype
Francesco Pietra
francesco.pietra at accademialucchese.it
Mon Oct 5 22:05:31 CEST 2009
On Mon, Oct 5, 2009 at 8:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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?
http://md.chem.rug.nl/~marrink/coarsegrain.html
>
>> 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.
The .mdp I used is not from a tutorial; it is the general purpose - or
standard - mdp provided by Martini. It doe not contain the word
"protein"
The "protein-in-vacuum.mdp from the ubiquitin CG tutoria does contain
both "Protein" and "Non-Protein" words. deleting "Non-Protein", the
error from running grompp is:
Fatal error:
Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values
>
>> 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.
I fully agree. Using "protein-in-vacuum.mdp", although attractive
because of "vacuum", was a bold adventure. But the standard mdp I used
before is declared to be standard, and my protein is standard. As I
said, I'll work hard to come out but before I'll take a few days
wandering with my Brittany on the Alps. The Tetraonidae will refresh
my mind.
Thanks for all you did for me (for us)
francesco
>
> -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
>>>>>>>
>>>>>>> ========================================
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>
>>>>> ========================================
>>>>> _______________________________________________
>>>>> 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
>>>>>
>>>>>
>>> --
>>> ========================================
>>>
>>> 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
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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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