[gmx-users] how to write the correct top file for membrane protein system?

[Justin A. Lemkul]

Quoting liang <petrucci123 at vip.sina.com>:

> Dear User,
>
> i try to perform simulation on membrane protein ( proterin + DPPC ).
> And i use OPLS for protein, Berger force field for DPPC.
> But after i construct this system, i cannot obtain tpr file by using grompp.
>
> Here is my topol.top :
>
> ; protein
> #include "ffoplsaa.itp"
> #include "protein-opls.itp"
>
> ; membrane
> #include "ffgmx.itp"
> #include "lipid.itp"
> #include "dppc.itp"
>
> ; Include water topology
> #include "spc.itp"
>
> [ system ]
> ; name
> Membrane in water
>
> [ molecules ]
> ; name  number
> Protein        1
> DPPC      123
> SOL     14189
>
> here is the result:
>
--------------------------------------------------------------------------------------------------------------------
> Fatal error:
> Invalid order for directive defaults, file
> ""/home/gmx331/share/gromacs/top/ffgmx.itp"", line 4
>
--------------------------------------------------------------------------------------------------------------------

I suspect it is a result of using two different force fields.  The [ defaults ]
will be defined in the first force field (in your case, ffoplsaa.itp), but then
grompp is finding a second [ defaults ] in ffgmx.itp.  See here:

http://wiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file

-Justin

>
> Could you please give me some suggestion?  i appreciate your help.
>
> Thanks so much!



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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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