[gmx-users] pdb2gmx -water-> grompp
ppirzade at ucalgary.ca
Wed Aug 19 00:40:43 CEST 2009
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?
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):
> > 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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