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

[Ahmet yıldırım]

I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from
gromacs 4.0.7. are they wrong?


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