Re: [gmx-users] Invalid order for directive X

[Mark Abraham]

Hi,

The output files from acpype I mean.

Mark

On Mon, Jul 10, 2017 at 3:59 PM Khadija Amine  wrote:

> Hi Mark,
>
> Thank you for your quick reply.
>
> You mean by 'the acpype files must be edited to have all the atom types in
> a block before any of the molecules' all the files with GMX as I have used
> amberff99sb.
>
> There are many files for charmm, opls, ...
>
> In my case, I should see the following files: ACT_GMX.gro. ACT_GMX.itp,
> ACT_NEW.pdb ?
>
> Khadija
>
>
> *​Khadija Amine*
> Ph.D. Biology and Health
> Biochemistry & Bioinformatics
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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[gmx-users] Invalid order for directive X

[Khadija Amine]

Hi Mark,

Thank you for your quick reply.

You mean by 'the acpype files must be edited to have all the atom types in
a block before any of the molecules' all the files with GMX as I have used
amberff99sb.

There are many files for charmm, opls, ...

In my case, I should see the following files: ACT_GMX.gro. ACT_GMX.itp,
ACT_NEW.pdb ?

Khadija


*​Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
-- 
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Re: [gmx-users] Invalid order for directive X

[Mark Abraham]

Hi,

The atomtypes directive must appear early. So the acpype files must be
edited to have all the atom types in a block before any of the
moleculetypes. This is covered specifically at
http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx


Mark



On Mon, 10 Jul 2017 13:35 Khadija Amine  wrote:

> Hello,
>
> I have read the documentation and tried to solve the problem but still
> having the same error.
>
> Any suggestions, please?
>
>
> *Khadija Amine*
> Ph.D. Biology and Health
> Biochemistry & Bioinformatics
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Invalid order for directive X

[Khadija Amine]

Hello,

I have read the documentation and tried to solve the problem but still
having the same error.

Any suggestions, please?


*Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
-- 
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Re: [gmx-users] Invalid order for directive X

[Nikhil Maroli]

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx
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[gmx-users] Invalid order for directive X

[Khadija Amine]

Dear gromacs 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   fcxfcyfcz
   11   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_A21
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
 cc   0.0  0.0   A 3.39967e-01   3.59824e-01 ;
1.91  0.0860
 oo   0.0  0.0   A 2.95992e-01   8.78640e-01 ;
1.66  0.2100
 oh   oh  0.0  0.0   A 3.06647e-01   8.80314e-01 ;
1.72  0.2104
 c3   c3  0.0  0.0   A 3.39967e-01   4.57730e-01 ;
1.91  0.1094
 ho   ho  0.0  0.0   A 0.0e+00   0.0e+00 ;
0.00  0.
 hc   hc  0.0  0.0   A 2.64953e-01   6.56888e-02 ;
1.49  0.0157

 [ moleculetype ]
 ;namenrexcl
  ACT  3

 [ atoms ]
 ;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
  1c 1   ACTC11 0.623101 12.01000 ; qtot 0.623
  2o 1   ACTO12-0.485000 16.0 ; qtot 0.138
  3   oh 1   ACTO23-0.584101 16.0 ; qtot -0.446
  4   c3 1   ACTC24-0.200100 12.01000 ; qtot -0.646
  5   ho 1   ACTH15 0.422000  1.00800 ; qtot -0.224
  6   hc 1   ACTH26 0.074700  1.00800 ; qtot -0.149
  7   hc 1   ACTH37 0.074700  1.00800 ; qtot -0.075
  8   hc 1   ACTH48 0.074700  1.00800 ; qtot -0.000

 [ bonds ]
 ;   ai aj funct   r k
  1  2   11.2183e-015.3363e+05 ; C1 - O1
  1  3   11.3513e-013.3480e+05 ; C1 - O2
  1  4   11.5241e-012.6192e+05 ; C1 - C2
  3  5   19.7300e-023.1079e+05 ; O2 - H1
  4  6   11.0969e-012.7665e+05 ; C2 - H2
  4  7   11.0969e-012.7665e+05 ; C2 - H3
  4  8   11.0969e-012.7665e+05 ; C2 - H4

 [ pairs ]
 ;   ai ajfunct
  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 akfunct   theta cth
  1  3  5  11.0655e+024.1740e+02 ; C1 - O2
- H1
  1  4  6  11.0877e+023.9271e+02 ; C1 - C2
- H2
  1  4  7  11.0877e+023.9271e+02 ; C1 - C2
- H3
  1  4  8  11.0877e+023.9271e+02 ; C1 - C2
- H4
  2  1  3  11.2210e+026.3530e+02 ; O1 - C1
- O2
  2  1  4  11.2320e+025.6400e+02 ; O1 - C1
- C2
  3  1  4  11.1273e+025.7237e+02 ; O2 - C1
- C2
  6  4  7  11.0758e+023.2970e+02 ; H2 - C2
- H3
  6  4  8  11.0758e+023.2970e+02 ; H2 - C2
- H4
  7  4  8  11.0758e+023.2970e+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   0.0   0 ; O1-C1-
   C2-H2
  2  1  4  6  9 0.00   3.34720   1 ; O1-C1-
   C2-H2
  2  1  4  6  9