> Date: Mon, 26 Jul 2010 07:26:04 -0400
> From: [email protected]
> To: [email protected]
> Subject: Re: [gmx-users] Problem in setup energy minimization step(grompp)
>
>
>
> X Rules wrote:
> > Precisely,
> >
> > open your xyz.top file and search for #include "spc.itp" and replace
> > this line with #include "tip4p.itp"
> >
> > and you will be done with.
> >
>
> Not if the coordinates present are for a three-point water model, in which
> case
> the same error is occurring. If you're switching models like this, you have
> to
> re-build the system.
agreed, but I build my system entirely for tip4p, i.e adding tip4p using genbox
and still my top file contains spc.itp instead of tip4p.itp (possible bug?? in
4.0.5 alteast).
>
> -Justin
>
> >
> >
> > > Date: Mon, 26 Jul 2010 07:00:57 -0400
> > > From: [email protected]
> > > To: [email protected]
> > > Subject: Re: [gmx-users] Problem in setup energy minimization
> > step(grompp)
> > >
> > >
> > >
> > > [email protected] wrote:
> > > >
> > > > Hi all,
> > > > I am facing a problem when i tried the TIP4P water model
> > > > for the set up of energy minimization using grompp.
> > > > This error did'nt occur while using the spce model.
> > > >
> > > > Fatal error:
> > > > number of coordinates in coordinate file (1.pdb, 31975)
> > > > does not match topology (1.top, 24795)
> > > > Please help me to rectify this problem.
> > > >
> > >
> > > So all you did was change the water model? That would certainly
> > explain it,
> > > since SPC/E is a 3-point model, and TIP4P has 4 sites. Otherwise:
> > >
> > >
> > http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
> > >
> > > -Justin
> > >
> > > > Thanks
> > > > Bipin
> > >
> > > --
> > > ========================================
> > >
> > > Justin A. Lemkul
> > > Ph.D. Candidate
> > > ICTAS Doctoral Scholar
> > > MILES-IGERT Trainee
> > > 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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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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