[gmx-users] tip5p water model:Atomtype LP1 not found

[Justin Lemkul]

On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım <ahmedo047 at gmail.com> wrote:

> I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from
> gromacs 4.0.7. are they wrong?
>
>
Well, they trigger a fatal error...

Yes, they are wrong and newer versions of Gromacs are correct.

-Justin


>
> 2013/4/11 Justin Lemkul <jalemkul at vt.edu>
>
> > On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım <ahmedo047 at gmail.com>
> > wrote:
> >
> > > Dear Justin,
> > >
> > > I copied to gmx.ff it. You know the tip5p shows the general shape of
> the
> > > 5-site water models but the spc shows the general shape of the 3-site
> > water
> > > models. Therefore I need tip5p.itp.
> > >
> >
> > Is there going to be a protein in the system, as well? If so, gmx.ff is a
> > poor choice and I would still maintain that despite any possible
> > improvement in water model (and none of them are perfect), it's not a
> > proper combination. If you're simulating pure water, the choice of parent
> > force field is largely irrelevant.
> >
> >
> > > How can you get it?
> > >
> > >
> > I have no idea why your tip5p.itp is wrong. The atom type should be MW
> for
> > both LP1 and LP2, as I said before. Fix the atom types and the problem
> > should go away.
> >
> > -Justin
> >
> >
> > >
> > > 2013/4/11 Justin Lemkul <jalemkul at vt.edu>
> > >
> > > > On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım <ahmedo047 at gmail.com
> >
> > > > wrote:
> > > >
> > > > > Dear users,
> > > > >
> > > > > I am trying MD simulation of tip5p water model. I am getting Fatal
> > > > > Error:Atomtype LP1 not found.
> > > > > There isnt LP in atomtypes.atp file. Which one corresponds to LP1
> and
> > > LP2
> > > > > atoms in atomtypes.atp file?
> > > > > (I am using Gromacs 4.5.5)
> > > > >
> > > > >
> > > > > usr/share/gromacs/top/gmx.ff/tip5p.itp
> > > > > ...
> > > > > [ atoms ]
> > > > > ; id    at type res nr  residu name     at name         cg nr
> > charge
> > > > > 1       OW            1       SOL              OW             1
> >   0
> > > > > 2       HW1              1       SOL             HW1             1
> > > > > 0.241
> > > > > 3       HW2           1       SOL             HW2             1
> > > > 0.241
> > > > > 4       LP1           1       SOL             LP1             1
> > > >  -0.241
> > > > > 5       LP2           1       SOL             LP2             1
> > > >  -0.241
> > > > > ....
> > > > >
> > > > >
> > > > It looks like someone has erroneously modified your files. The TIP5P
> > > model
> > > > should not be included in gmx.ff (Gromos force fields should be used
> > with
> > > > SPC), and the atom type for both LP1 and LP2 should be MW.
> > > >
> > > > -Justin
> > > >
> > > > --
> > > >
> > > > ========================================
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Research Scientist
> > > > Department of Biochemistry
> > > > Virginia Tech
> > > > Blacksburg, VA
> > > > jalemkul[at]vt.edu | (540)
> > > > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > >
> > > > ========================================
> > > > --
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> > >
> > >
> > >
> > > --
> > > Ahmet Yıldırım
> > > --
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> >
> >
> >
> > --
> >
> > ========================================
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540)
> > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
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>
>
> --
> Ahmet Yıldırım
> --
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-- 

========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================