X Rules wrote:
> 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).
There is no bug. The default water model written to the topology is spc.itp,
but this can be chosen when running pdb2gmx with the -water flag. The mechanism
for choosing water models will be completely different in the upcoming version
of GROMACS, such that the choice will be completely user-dependent.
-Justin
>
> -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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--
========================================
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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