[gmx-users] Error in generating DPPC using grompp
Justin A. Lemkul
jalemkul at vt.edu
Mon Jan 24 14:40:06 CET 2011
shobana visolingam wrote:
> thanks. i read chapter 5 and i saw the DPPC topology in the membrane
> protein tutorial but i still cant find what's wrong with my topology
> format.
> below is how my topol.top file looks like
>
> #include "ffgmx_lipid.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Protein_A 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 CH3 1 DPPC C1 1 0.124 15.035 ;
<snip>
> ; Include DPPC chain topology
> #include "DPPC.itp"
>
This doesn't make any sense. You've defined a "Protein_A" moleculetype
containing DPPC, then you're including a chain topology for it (again) here.
<snip>
> *and my ffgmxbon_lipid.itp file is:*
>
> [ bondtypes ]
> ; i j func b0 kb
> C O 1 0.12300 502080.
> C OM 1 0.12500 418400.
> C OA 1 0.13600 376560.
> C N 1 0.13300 418400.
> C NT 1 0.13300 376560.
> C NL 1 0.13300 376560.
> CH1 OA 1 0.14300 334720.
> CH1 N 1 0.14700 376560.
> CH1 NT 1 0.14700 376560.
> CH1 NL 1 0.14700 376560.
> CH1 C 1 0.15300 334720.
> CH1 CH1 1 0.15300 334720.
> CH2 OM 1 0.14300 376560.
> CH2 OA 1 0.14300 334720.
> ................................................
> ................................................
>
> ; get the constraint distances:
> #include "ff_dum.itp"
>
> [ constrainttypes ]
> ; now the constraints for the rigid NH3 groups
> MNH3 C 2 DC_MNC1
> MNH3 CB 2 DC_MNC1
> MNH3 CHE 2 DC_MNC1
> MNH3 CH1 2 DC_MNC2
> MNH3 CH2 2 DC_MNC2
> MNH3 MNH3 2 DC_MNMN
> ; and the angle-constraints for OH and SH groups in proteins:
> CH2 HS 2 DC_CS
> CH2 HO 2 DC_CO
> CH1 HO 2 DC_CO
> CB HO 2 DC_CO
> C HO 2 DC_CO
> P HO 2 DC_PO
>
> [ angletypes ]
> ; i j k func th0 cth
> HO OA C 1 109.500 397.480
> HO OA CH1 1 109.500 397.480
> HO OA CH2 1 109.500 397.480
> HO OA CB 1 109.500 397.480
> HO OA CHE 1 109.500 397.480
> P OA HO 1 109.500 397.480
> CS1 OA HO 1 109.500 397.480
> CS2 OA HO 1 109.500 397.480
> HW OW HW 1 109.500 502.080
> CH1 N C 1 122.000 502.080
> CH2 N C 1 122.000 502.080
> CH2 N CH1 1 116.000 502.080
> CH3 N C 1 117.000 502.080
> CH3 N CH1 1 125.000 502.080
> CH3 N CH2 1 125.000 502.080
> H N C 1 123.000 292.880
> ..................................................
> ..................................................
>
> [ dihedraltypes ]
> ; i l func q0 cq
> NR5* NR5 2 0.000 167.360
> NR5* NR5* 2 0.000 167.360
> C O 2 0.000 167.360
> C OM 2 0.000 167.360
> C NT 2 0.000 167.360
> .............................................
> .............................................
> ............................................
>
>
> [ dihedraltypes ]
> ; j k func phi0 cp mult
> C OA 1 180.000 16.736 2
> C N 1 180.000 33.472 2
> C NT 1 180.000 33.472 2
> C NL 1 0.000 3.766 3
> CH1 OA 1 0.000 1.255 3
> CH1 N 1 180.000 0.418 6
> CH1 NT 1 0.000 3.766 6
> CH1 NL 1 0.000 3.766 3
> CH1 C 1 0.000 0.418 6
> CH1 CH1 1 0.000 5.858 3
> CH2 OA 1 0.000 1.255 3
> CH2 N 1 180.000 0.418 6
> CH2 NT 1 0.000 3.766 6
> CH2 NL 1 0.000 3.766 3
> CH2 C 1 0.000 0.418 6
> CH2 CH1 1 0.000 5.858 3
> CH2 CH2 1 0.000 5.858 3
> CB OA 1 180.000 7.113 2
> CB NT 1 180.000 33.472 2
> CB C 1 180.000 5.858 2
> CB CH2 1 0.000 0.418 6
> CB CR61 1 180.000 41.840 2
> CHE OA 1 180.000 7.113 2
> CHE NT 1 180.000 33.472 2
> CHE C 1 180.000 5.858 2
> CHE CH2 1 0.000 0.418 6
> CHE CR61 1 180.000 41.840 2
> S CH2 1 0.000 2.929 3
> S S 1 0.000 16.736 2
> FE NR5 1 0.000 0.000 4
> NZ C 1 180.000 33.472 2
> NE C 1 180.000 33.472 2
> NE CH2 1 180.000 0.418 6
> ; two or three dihedral potentials are needed over some bonds,
> ; put the parameters in your topology manually
> ; P OA 1 0.000 1.046 3
> ; P OA 1 0.000 3.138 2
> OS CH2 1 0.000 3.766 3
> ; OS P 1 0.000 1.046 3
> ; OS P 1 0.000 3.138 2
> CS1 OA 1 0.000 1.255 3
> CS1 NR5* 1 0.000 0.000 2
> CS1 CH2 1 0.000 5.858 3
> CS1 OS 1 0.000 3.766 3
> ; CS1 CS1 1 0.000 5.858 3
> ; CS1 CS1 1 0.000 0.418 2
> ; CS1 CS1 1 0.000 2.092 2
> NR6 CB 1 180.000 33.472 2
> NR6 CHE 1 180.000 33.472 2
> NR6* CH2 1 0.000 0.418 6
> NR6* CB 1 180.000 33.472 2
> NR6* CHE 1 180.000 33.472 2
> NR6* CS1 1 0.000 0.000 2
> CS2 OA 1 0.000 1.255 3
> CS2 OS 1 0.000 3.766 3
> ; CS2 CS1 1 0.000 5.858 3
> ; CS2 CS1 1 0.000 0.418 2
> ; CS2 CS1 1 0.000 2.092 2
> SI CH1 1 0.000 5.858 3
> SI OS 1 0.000 3.766 3
> C CP2 1 0.000 0.418 6
> CH1 OS 1 0.000 3.766 3
> C OS 1 0.000 3.766 3
> CP2 CP2 1 0.000 0.418 6
>
> [ dihedraltypes ]
> CP2 CP2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
> CH2 CH2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
> LP2 LP2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
> LH2 LH2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
>
> #define ANG_180_0 180 0
> #define DIH_0_0_2 0 0 2
> [DPPC]
> [atoms]
Here you're including an .rtp entry in the topology that should hold only bonded
parameters. This is where the error originates; you've pasted together two
entirely different files.
-Justin
> C1 CH3 0.124 0
> C2 CH3 0.124 0
> C3 CH3 0.124 0
> N4 NL 0.004 0
> C5 CH2 0.124 0
> C6 CH2 0.000 1
> O7 OS -0.180 2
> P8 P 0.500 2
> O9 OM -0.320 2
> O10 OM -0.320 2
> O11 OS -0.180 2
> C12 CH2 0.000 3
> C13 CH1 0.100 4
> O14 OS -0.180 4
> C15 C 0.270 4
> O16 O -0.190 4
> C17 CH2 0.000 5
> C18 CH2 0.000 6
> C19 CH2 0.000 7
> C20 CH2 0.000 8
> C21 CH2 0.000 9
> C22 CH2 0.000 10
> C23 CH2 0.000 11
> C24 CH2 0.000 12
> C25 CH2 0.000 13
> .......................................
> .....................................
> ......................................
>
> [ bonds ]
> C1 N4 gb_21
> C2 N4 gb_21
> C3 N4 gb_21
> N4 C5 gb_21
> C5 C6 gb_27
> C6 O7 gb_18
> O7 P8 gb_28
> P8 O9 gb_24
> P8 O10 gb_24
> P8 O11 gb_28
> .....................................
> ......................................
> [ angles ]
> ; ai aj ak gromos type
> O33 N4 C34 ga_13
> O33 N4 O35 ga_13
> O33 N4 C32 ga_13
> C34 N4 O35 ga_13
> C34 N4 C32 ga_13
> O35 N4 C32 ga_13
> N4 C32 C31 ga_15
> C32 C31 C32 ga_15
> C31 C32 P8 ga_26
> C32 P8 O33 ga_14
> C32 P8 C34 ga_14
> C32 P8 C31 ga_5
> O33 P8 C34 ga_29
> O33 P8 C31 ga_14
> C34 P8 C31 ga_14
> P8 C31 C3 ga_26
> C31 C3 C2 ga_15
> C3 C2 C21 ga_13
> .....................................
> ...................................
>
> [ impropers ]
> ; ai aj ak al gromos type
> C13 O14 C32 C12 gi_2
> C15 O14 C17 O16 gi_1
> C34 O33 C36 O35 gi_1
> [ dihedrals ]
> ; ai aj ak al gromos type
> O33 N4 C32 C31 gd_29
> N4 C32 C31 C32 gd_4
> N4 C32 C31 C32 gd_36
> C32 C31 C32 P8 gd_29
> C31 C32 P8 C31 gd_20
> C31 C32 P8 C31 gd_27
> C32 P8 C31 C3 gd_20
> C32 P8 C31 C3 gd_27
> P8 C31 C3 C2 gd_29
> .......................................
> ..........................................
>
>
> > Date: Fri, 21 Jan 2011 06:53:42 -0500
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Error in generating DPPC using grompp
> >
> >
> >
> > shobana visolingam wrote:
> > >
> > >
> > >
> ------------------------------------------------------------------------
> > >
> > >
> > > dear all,
> > >
> > > i am new to gromacs and i'm trying to run the command grompp -c
> > > lipo1grobox.pdb -p topol.top -f em_restraints.mdp -o em_restraints.tpr.
> > >
> > > however i got this error
> > >
> > > *Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
> > >
> > > ERROR 1 [file ffgmxbon_lipid.itp, line 756]:
> > > Invalid directive DPPC
> > >
> > >
> > > -------------------------------------------------------
> > > Program grompp, VERSION 4.0.4
> > > Source code file: topio.c, line: 415
> > >
> > > Fatal error:
> > > Syntax error - File ffgmxbon_lipid.itp, line 757
> > > Last line read:
> > > '[atoms]'
> > > Invalid order for directive atoms*
> > >
> > >
> > > can i know what this error mean and how to overcome it?? thanks.
> > >
> >
> > You have serious errors in your topology. Without seeing it, there's
> nothing
> > else anyone can really suggest except for having a thorough read
> through Chapter
> > 5. The topology must follow a specific order, which you likely have not
> > followed. A simple DPPC topology is available as part of my membrane
> protein
> > tutorial:
> >
> > http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > 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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--
========================================
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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