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

[liang]

Hi Hadas,

i have tried to use gromos87 for protein, everything is ok. (just with ffgmx.itp)
but if i use opls for protein, i have to add "ffoplsaa.itp" in top file, otherwise it cannot provide some parameters for protein.
Did you use gromos87 to generate your protein itp files (chain_A .itp ...) ?

Thanks

Liang

----- Original Message ----- 
From: "Hadas Leonov" <hleonov at cc.huji.ac.il>
To: "liang" <petrucci123 at vip.sina.com>; "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Sunday, November 25, 2007 5:26 PM
Subject: Re: [gmx-users] how to write the correct top file for membraneprotein system?


> Hi Liang,
> 
> Do you have to define ffoplsaa.itp in your top file? isn't it enough to 
> generate your protein topology with the OPLS forcefield using pdb2gmx and 
> include the protein's generated itp files?
> 
> I don't use OPLS, but my own definition of the .top file goes like this:
> 
> ; generic + lipid topology
> #include "ffgmx.itp"
> #include "lipid.itp"
> #include "dmpc.itp"
> #include "ions.itp"
> 
> ; protein
> #include "chain_A.itp"
> #include "chain_B.itp"
> #include "chain_C.itp"
> #include "chain_D.itp"
> 
> ; water
> #include "spc.itp"
> 
> Rest of my molecule definitions are similar (protein first, then lipid, then 
> water, and finally ions to neutralize the system).
> 
> Hope it helps,
> Hadas.
> ----- Original Message ----- 
> From: "liang" <petrucci123 at vip.sina.com>
> To: "Justin A. Lemkul" <jalemkul at vt.edu>
> Cc: <gmx-users at gromacs.org>
> Sent: Sunday, November 25, 2007 7:41 AM
> Subject: Re: [gmx-users] how to write the correct top file for 
> membraneprotein system?
> 
> 
>> 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/
>>>
>>> ========================================
>>>
>>
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> 
>