[gmx-users] pdb2gmx -water-> grompp; grompp error

[Paymon Pirzadeh]

Hello,
Just a reminder that I had troubled with combination rules between my
water model and GROMACS forcefields. I fixed the problem by adjusting my
water model's parameters. BUT, now, I specified the new parameters in
my .itp file under [ atomtype ] category and grompp makes errors out of
the orders. Now I am using OPLSaa. I suspect again the problem comes
from the presence of the second [atomtype ]. How can I keep my new
parameters and use them in my water model's itp file? Or should I change
these parameters in the OPLSaa.itp file? 
Regards,

Payman  










On Wed, 2009-08-19 at 10:20 +1000, Mark Abraham wrote:
> Paymon Pirzadeh wrote:
> > 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)?
> 
> A water model that isn't compatible with the model of the solutes isn't 
> of any value, so it looks like you have put the cart before the horse.
> 
> Mark
> 
> > 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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> >>>
> > 
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