[gmx-users] Error - syntax

[Chang Woon Jang]

Dear Mark,

   Thank you for the information. I have changed the topol.top file now like

I put another three lined for posres right below each itp, DGA.itp and
J230.itp.

; Include forcefield parameters
;#include "forcefield.itp"

; Include chain topologies
#include "DGA.itp"
#ifdef POSRES
#include "porse_A.itp"
#endif

#include "J230.itp"
#ifdef POSRES
#include "porse_B.itp"
#endif

[ system ]
; Name
Built with Packmol

[ molecules ]
; Compound        #mols
Other_chain_A       200
Other_chain_B       100


   In the DGA.itp file,

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1             1               no              0.0     0.0

[ atomtypes ]
;type    mass    charge       ptype          sigma      epsilon
 B     42.080999  0.000       A        1.000000000  1.000000000
 A     151.18579  0.000       A        1.000000000  1.000000000

[ moleculetype ]
Other_chain_A 3

[atoms]
; nr type resnr residue atom cgnr charge mass
1 A 1 RES A1 1 0.000000 151.18579
2 A 1 RES A2 2 0.000000 151.18579
3 B 1 RES B1 3 0.000000 42.080999


[ bonds ]
1 3   8   1 1.0; 1:bond:1
2 3   8   1 1.0; 1:bond:2

[ angles ]
1 3 2   8  1 1.0  ; 1:angle:1



In J230.itp file,

[ atomtypes ]
;type    mass    charge       ptype          sigma      epsilon
 D     100.16139  0.000       A        1.000000000  1.000000000
 C     74.103099  0.000       A        1.000000000  1.000000000

[ moleculetype ]
Other_chain_B 3

[atoms]
; nr type resnr residue atom cgnr charge mass
1 C 1 RES C1 1 0.000000 74.103099
2 D 1 RES D1 2 0.000000 100.16139
3 C 1 RES C2 3 0.000000 74.103099


[ bonds ]
1 2   8  1  1.0  ; 1:bond:1
2 3   8  1  1.0  ; 1:bond:2

[ angles ]
1 2 3   8   1  1.0 ; 1:angle:1


The error still occurred as follow.

-------------------------------------------------------
Program gmx, VERSION 5.0.8-dev-20151014-1f04b58
Source code file:
/home/chang/PACKAGE/votca/src/gromacs/src/gromacs/gmxpreprocess/topio.c,
line: 727

Fatal error:
Syntax error - File J230.topfile.itp, line 5
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------


Don't I understand the passage correctly you linked?

Thank you.

Best regards,
Changwoon Jang




On Mon, Jan 25, 2016 at 1:34 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> See
> http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx
>
> Mark
>
> On Mon, 25 Jan 2016 19:19 Chang Woon Jang <changwoonjang at gmail.com> wrote:
>
> > Dear Gromacs Users,
> >
> >  I have two types of molecules. The topology file was separated by one
> > (topol.top) and two (DGA.itp, and J230.itp).
> >
> > The format I made in topol.top is
> >
> > #include "DGA.itp"
> > #include "J230.itp"
> >
> > [ system ]
> > ; Name
> > DGA and J230
> >
> > [ molecules ]
> > ; Compound        #mols
> > Other_chain_A      200
> > Other_chain_B      100
> >
> > In the DGA.itp and J230.itp files, I formatted like but only difference
> > between DGA.itp and J230.tip is type (C and D) and mass.
> >
> >
> > [ defaults ]
> > ; nbfunc    comb-rule   gen-pairs    fudgeLJ  fudgeQQ
> >   1             1                 no               0.0         0.0
> > [ atomtypes ]
> > ; type    mass           charge     ptype             sigma       epsilon
> >  B         42.090999    0.000      A                    1.0000     1.0000
> >  A         151.185798  0.000      A                    1.0000     1.0000
> >
> > [ molecuetype ]
> > Other_chain_A 3
> >
> > [atoms]
> > ; nr type resnr residue atom cgnr charge mass
> > 1 A 1 RES A1 1 0.00000 151.185798
> > 2 A 1 RES A2 2 0.00000 151.185798
> > 3 B 1 RES B1 3 0.00000 42.080999
> >
> > [ bonds ]
> > 1 3    8   1   1.0 ; 1:bond:1
> > 2 3    8   1   1.0 ; 1:bond:2
> >
> > [ angles ]
> > 1 3 2   8   1  1.0    ; 1:angle:1
> >
> > An error says,
> >
> > Fatal error:
> > Syntax error - file DGA.itp, line 1
> > Last line read:
> > ' [ defaults ]'
> > invalid order for directive moleculetype
> > For more .....
> >
> >
> > I am trying to simulate a Coarse-grained model and the topology file was
> > created. I think that the formatting is correct following an example from
> > votca coarse graining tool. When I use two type of molecules in atomistic
> > scale, these separated topology files work fine.
> >
> > Would you please what the correct format of this to be run?
> >
> > Thank you very much for your advise.
> >
> >
> > Best regards,
> > Changwoon Jang,
> > --
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