[gmx-users] tip5p water model:Atomtype LP1 not found
Ahmet yıldırım
ahmedo047 at gmail.com
Thu Apr 11 13:28:48 CEST 2013
There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I couldnt
find them
2013/4/11 Justin Lemkul <jalemkul at vt.edu>
> 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
> > --
> > gmx-users mailing list gmx-users at gromacs.org
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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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--
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