[gmx-users] Error: Expected a molecule type name and nrexcl

[Justin A. Lemkul]

Steven Neumann wrote:
> Dear Gmx Users,
>  
> I have built my system which includes a tube and a protein. I 
> represented my tube as carbon atoms using Charmm27 ff. I processed 
> pdb2gmx for a tube and protein togehter and divide it into two itp 
> files including it in my topoloy file:
>  
> 
> ; Include forcefield parameters
> 
> #include "./charmm27mod.ff/forcefield.itp"
> 
> ; Include tube topology
> 
> #include "Tubes.itp"
> 
> ; Include Position restraint of Tube
> 
> #ifdef POSRES_T
> 
> #include "posreTubes.itp"
> 
> #endif
> 
> ; Include Protein topology
> 
> #include "Protein.itp"
> 
> ; Include Position restraint of Protein
> 
> #ifdef POSRES_P
> 
> #include "posreProtein.itp"
> 
> #endif
> 
> ; Include Position restraint file
> 
> #ifdef POSRES
> 
> #include "posreALL.itp"
> 
> #endif
> 

What is this file?  Note that you can't apply position restraints to multiple 
[moleculetypes] so if that's what you're trying, don't (see the manual).

> ; Include water topology
> 
> #include "./charmm27mod.ff/tip3p.itp"
> 
> #ifdef POSRES_WATER
> 
> ; Position restraint for each water oxygen
> 
> [ position_restraints ]
> 
> ; i funct fcx fcy fcz
> 
> 1 1 1000 1000 1000
> 
> #endif
> 
> ; Include topology for ions
> 
> #include "./charmm27mod.ff/ions.itp"
> 
> [ system ]
> 
> ; Name
> 
> Protein in water
> 
> [ molecules ]
> 
> ; Compound #mols
> 
> Protein_chain_X 1
> 
> Tubes_chain_X 1
> 
> Then I added 23000 water molecules and trying to process grompp in order 
> to replace water molecules with ions obtained errors:
> 
> ERROR 1 [file Protein.itp, line 6]:
>   Expected a molecule type name and nrexcl
> 
> 
> ERROR 2 [file Protein.itp, line 7]:
>   Expected a molecule type name and nrexcl
> 
> .....
> 
>  
> 
> My Protein.itp file is copied from topol.top file and 1st lines look like:
> 
> [ moleculetype ]
> 
> ; Name nrexcl
> 
> Protein_chain_X 3
> 

There should be an [atoms] directive in here.  You can't declare atoms in a 
[moleculetype] directive.  Which line is #6, where the error occurs?

> ; residue 1009 MET rtp MET q 0.0
> 
> 1009 NH2 1009 MET N 1009 -0.96 14.007 ; qtot -0.96
> 
> 1010 H 1009 MET HT1 1010 0.34 1.008 ; qtot -0.62
> 
> 1011 H 1009 MET HT2 1011 0.34 1.008 ; qtot -0.28
> 
> 1012 CT1 1009 MET CA 1012 0.19 12.011 ; qtot -0.09
> 
> 1013 HB 1009 MET HA 1013 0.09 1.008 ; qtot 0
> 
> 1014 CT2 1009 MET CB 1014 -0.18 12.011 ; qtot -0.18
> 
> 1015 HA 1009 MET HB1 1015 0.09 1.008 ; qtot -0.09
> 
> 1016 HA 1009 MET HB2 1016 0.09 1.008 ; qtot 0
> 
> 1017 CT2 1009 MET CG 1017 -0.14 12.011 ; qtot -0.14
> 
> 1018 HA 1009 MET HG1 1018 0.09 1.008 ; qtot -0.05
> 
> 1019 HA 1009 MET HG2 1019 0.09 1.008 ; qtot 0.04
> 
> 1020 S 1009 MET SD 1020 -0.09 32.06 ; qtot -0.05
> 
> 1021 CT3 1009 MET CE 1021 -0.22 12.011 ; qtot -0.27
> 
> 1022 HA 1009 MET HE1 1022 0.09 1.008 ; qtot -0.18
> 
> 1023 HA 1009 MET HE2 1023 0.09 1.008 ; qtot -0.09
> 
> 1024 HA 1009 MET HE3 1024 0.09 1.008 ; qtot 0
> 
> 1025 C 1009 MET C 1025 0.51 12.011 ; qtot 0.51
> 
> 1026 O 1009 MET O 1026 -0.51 15.999 ; qtot 0
> 
> Do you have any clue what is wrong?
> 
> Then another Error starting from the 1st (1009) atom of my protein:
> 
> Atom index (1009) in bonds out of bounds (1-0).
> This probably means that you have inserted topology section "bonds"
> in a part belonging to a different molecule than you intended to.
> In that case move the "bonds" section to the right molecule.
> 

My guess would be that this error comes from whatever is in "posreALL.itp," but 
that's just a hunch based on the file name.

> My tube is not connected with a protein. Should I turn off CMAP? Will it 
> affect it?
> 

There are no errors coming from CMAP.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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