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: [email protected]
> To: [email protected]
> 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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