[gmx-users] Error - syntax

[Mark Abraham]

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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