[gmx-users] grompp: no such moleculetype

Francesco Pietra francesco.pietra at accademialucchese.it
Mon Oct 5 19:29:21 CEST 2009 

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:

;
; 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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