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

[liang]

Dear Justin,

Thanks for you quickly reply.

I have tried before to comment out the section of [ defaults ] in the next 
itp file, but still too many warnings and final crashed.
And i think it would not be the best method to solve this problem, because i 
have to use ffgmx.itp to deal with DPPC.

Is there any other method i can try?

Thanks

Liang

----- Original Message ----- 
From: "Justin A. Lemkul" <jalemkul at vt.edu>
To: "liang" <petrucci123 at vip.sina.com>; "Discussion list for GROMACS users" 
<gmx-users at gromacs.org>
Sent: Sunday, November 25, 2007 12:23 PM
Subject: Re: [gmx-users] how to write the correct top file for membrane 
protein system?


> 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!
>
>
>
> ========================================
>
> 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/
>
> ========================================
>