[gmx-users] pdb2gmx -water-> grompp

[Paymon Pirzadeh]

I checked all the force-fields available in the GROAMCS. None of them
have the #2 combination rule which matches my water model! Any
alternatives (rather than changing my water model)?

Payman




On Tue, 2009-08-18 at 18:52 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > That was very helpful! But I realized a problem. The OPLSaa uses the
> > combination rule #3 in [ defaults ] while my water model uses #2. Now if
> > I comment out my water model's combination, I am not sure what I am
> > going to face! Any comments?
> > 
> 
> Then I would say that your water model's combination rule is inconsistent with 
> the method of nonbonded calculations in OPLS.  It appears that the only 
> difference between combination rules 2 and 3 comes when a specific interaction 
> is not defined in the [nonbond_params] section.  The specifics of these 
> combination rules are given in manual section 5.3.3.
> 
> -Justin
> 
> > Payman
> > 
> > 
> > 
> > 
> > On Tue, 2009-08-18 at 18:19 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> Well,
> >>> I changed the topology file of the system and manually typed the .itp of
> >>> my own water model. Just a reminder that I have used my own water
> >>> model's .itp file successfully in pure water systems. This .itp file
> >>> starts from [ defaults ] and contains all information needed. But when
> >>> it comes to grompp, the following error appears:
> >>>
> >>> Program grompp_d_mpi, VERSION 4.0.5
> >>> Source code file: topio.c, line: 415
> >>>
> >>> Fatal error:
> >>> Syntax error - File sixsitewater.itp, line 6
> >>> Last line read:
> >>> '[ defaults ]'
> >>> Invalid order for directive defaults
> >>>
> >> The only time that [defaults] should appear is in the force field that you are 
> >> calling (i.e., ffoplsaa.itp):
> >>
> >> http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults
> >>
> >> -Justin
> >>
> >>> I am trying to use this water model with OPLSaa. what kind of directive
> >>> am I missing? 
> >>>
> >>> Payman
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Tue, 2009-08-18 at 16:05 -0400, Justin A. Lemkul wrote:
> >>>> Paymon Pirzadeh wrote:
> >>>>> Hello,
> >>>>> I am trying to use a different water model for my proteins (using oplsaa
> >>>>> force field). I use the .itp file which I developed, but pdb2gmx does
> >>>>> not accept it. I am a bit confused on how I can make my water model work
> >>>>> with OPLSaa. Based on what I saw from spc.itp or other samples, do I
> >>>>> need to change the names of my particles in my water .itp file by
> >>>>> including _FF_OPLS?
> >>>> I don't know how pdb2gmx decides how to recognize water models; it may be 
> >>>> hard-coded.  In any case, your atom types have to be consistent with OPLS 
> >>>> standards; as for whether or not you need the #ifdef _FF_OPLS in your .itp file, 
> >>>> you may not need it if OPLS is the only force field with which it will be used. 
> >>>>   The #ifdef blocks just prevent a GROMOS system from trying to recognize OPLS, etc.
> >>>>
> >>>> -Justin
> >>>>
> >>>>> Regards,
> >>>>>
> >>>>> Payman 
> >>>>>
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> >>>
> > 
> > 
>