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

[Justin Lemkul]

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

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