[gmx-users] grompp: no such moleculetype

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 5 19:31:42 CEST 2009 


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.

-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
>>
>> ========================================
>> _______________________________________________
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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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