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

[Steven Neumann]

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

; 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

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

Thank you,

Steven
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