Question: Error with atomtypes in gromacs
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gravatar for kh.amine1
2.3 years ago by
kh.amine10
kh.amine10 wrote:

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

software error • 2.0k views
ADD COMMENTlink modified 2.3 years ago by WouterDeCoster41k • written 2.3 years ago by kh.amine10

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:

101010 Button

ADD REPLYlink written 2.3 years ago by WouterDeCoster41k

Thank you very much!

ADD REPLYlink written 2.3 years ago by kh.amine10
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