[gmx-users] grompp: no such moleculetype

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 5 23:14:18 CEST 2009 


Francesco Pietra wrote:

>> 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
> 

This comes up because you've defined one group now for T-coupling and assigned 
coupling constants and temperatures for two.  Haphazard changes to .mdp files 
will certainly generate these errors.  Deleting until the problem goes away 
never works - it only creates more problems :)

Please see the manual for proper use of tc-grps, etc.

>>> 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.
> 

What is "standard" for one user is not necessarily "standard" for another.  You 
must almost always make changes to suit your particular system, as a general rule.

> Thanks for all you did for me (for us)
> 

You're welcome.  Hopefully everything works out.

-Justin

> 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
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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
>>>>>> 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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>>>> interface
>>>> or send it to gmx-users-request at gromacs.org.
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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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>> or send it to gmx-users-request at gromacs.org.
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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

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

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