[gmx-users] grompp: no such moleculetype

[Francesco Pietra]

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.
============

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?


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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