Entering edit mode
6.8 years ago
kh.amine1
▴
10
Dear Biostar users,
I have a protein with two bound ligands, GNP and ACT. For the protein I have prepared topology with amber ff96. pdb2gmx created three itp files for the two protein chains and one for CA and MG ions.
Fore GNP and ACY I have generated itp files perfectly using acpype .When I have run gompp program for neutralisation step, I had this folowing error:
**Syntax error - File ACT.itp, line 3
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes It contains an [ atomtypes ] section defining the GAFF atom types.**
This was my complex topology file:
; Include forcefield parameters
#include "amber99sb.ff/forcefield.itp"
#include "ACT.itp"
#include "GNP.itp"
; Include chain topologies
#include "topolo_Protein_chain_A.itp"
#include "topolo_Protein_chain_B.itp"
#include "topolo_Ion_chain_A2.itp"
; Include water topology
#include "amber99sb.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 "amber99sb.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
Ion_chain_A2 1
GNP 1
ACT 1
SOL 20542
And this was my ACT.itp file:
; ACT_GMX.itp created by acpype (Rev: 10101) on Mon Jul 10 09:48:02 2017
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
c c 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
o o 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100
oh oh 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104
c3 c3 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094
ho ho 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000
hc hc 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157
[ moleculetype ]
;name nrexcl
ACT 3
[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot bond_type
1 c 1 ACT C1 1 0.623101 12.01000 ; qtot 0.623
2 o 1 ACT O1 2 -0.485000 16.00000 ; qtot 0.138
3 oh 1 ACT O2 3 -0.584101 16.00000 ; qtot -0.446
4 c3 1 ACT C2 4 -0.200100 12.01000 ; qtot -0.646
5 ho 1 ACT H1 5 0.422000 1.00800 ; qtot -0.224
6 hc 1 ACT H2 6 0.074700 1.00800 ; qtot -0.149
7 hc 1 ACT H3 7 0.074700 1.00800 ; qtot -0.075
8 hc 1 ACT H4 8 0.074700 1.00800 ; qtot -0.000
[ bonds ]
; ai aj funct r k
1 2 1 1.2183e-01 5.3363e+05 ; C1 - O1
1 3 1 1.3513e-01 3.3480e+05 ; C1 - O2
1 4 1 1.5241e-01 2.6192e+05 ; C1 - C2
3 5 1 9.7300e-02 3.1079e+05 ; O2 - H1
4 6 1 1.0969e-01 2.7665e+05 ; C2 - H2
4 7 1 1.0969e-01 2.7665e+05 ; C2 - H3
4 8 1 1.0969e-01 2.7665e+05 ; C2 - H4
[ pairs ]
; ai aj funct
2 5 1 ; O1 - H1
2 6 1 ; O1 - H2
2 7 1 ; O1 - H3
2 8 1 ; O1 - H4
3 6 1 ; O2 - H2
3 7 1 ; O2 - H3
3 8 1 ; O2 - H4
4 5 1 ; C2 - H1
[ angles ]
; ai aj ak funct theta cth
1 3 5 1 1.0655e+02 4.1740e+02 ; C1 - O2 - H1
1 4 6 1 1.0877e+02 3.9271e+02 ; C1 - C2 - H2
1 4 7 1 1.0877e+02 3.9271e+02 ; C1 - C2 - H3
1 4 8 1 1.0877e+02 3.9271e+02 ; C1 - C2 - H4
2 1 3 1 1.2210e+02 6.3530e+02 ; O1 - C1 - O2
2 1 4 1 1.2320e+02 5.6400e+02 ; O1 - C1 - C2
3 1 4 1 1.1273e+02 5.7237e+02 ; O2 - C1 - C2
6 4 7 1 1.0758e+02 3.2970e+02 ; H2 - C2 - H3
6 4 8 1 1.0758e+02 3.2970e+02 ; H2 - C2 - H4
7 4 8 1 1.0758e+02 3.2970e+02 ; H3 - C2 - H4
[ dihedrals ] ; propers
; for gromacs 4.5 or higher, using funct 9
; i j k l func phase kd pn
2 1 3 5 9 0.00 7.94960 1 ; O1- C1- O2- H1
2 1 3 5 9 180.00 9.62320 2 ; O1- C1- O2- H1
2 1 4 6 9 0.00 0.00000 0 ; O1- C1- C2- H2
2 1 4 6 9 0.00 3.34720 1 ; O1- C1- C2- H2
2 1 4 6 9 180.00 0.33472 3 ; O1- C1- C2- H2
2 1 4 7 9 0.00 0.00000 0 ; O1- C1- C2- H3
2 1 4 7 9 0.00 3.34720 1 ; O1- C1- C2- H3
2 1 4 7 9 180.00 0.33472 3 ; O1- C1- C2- H3
2 1 4 8 9 0.00 0.00000 0 ; O1- C1- C2- H4
2 1 4 8 9 0.00 3.34720 1 ; O1- C1- C2- H4
2 1 4 8 9 180.00 0.33472 3 ; O1- C1- C2- H4
3 1 4 6 9 180.00 0.00000 2 ; O2- C1- C2- H2
3 1 4 7 9 180.00 0.00000 2 ; O2- C1- C2- H3
3 1 4 8 9 180.00 0.00000 2 ; O2- C1- C2- H4
4 1 3 5 9 180.00 9.62320 2 ; C2- C1- O2- H1
[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
; i j k l func phase kd pn
3 1 2 4 4 180.00 4.60240 2 ; O2- C1- O1- C2
I have read and trying the folowing link but still having the same error.
http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx
Is it a mistake in the directives order in .itp and .top? Can someone give me a suggestion to fix the issue Thank you
I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:
Thank you very much!