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

[Hadas Leonov]

Yes, I used GROMOS87. Although it's deprecated now and I'm not sure
which ff to switch to. 

Hadas.

On Sun, 2007-11-25 at 19:03 +0800, liang wrote:
> 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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> >>
> >> -- 
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> >> 
> > 
> >