[gmx-users] grompp: no such moleculetype

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 5 16:39:09 CEST 2009 


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.

> 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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