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

[Hadas Leonov]

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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