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

[Ahmet yıldırım]

I have the following files in directory
1.tip5p.gro
2.topol.top
3.em.mdp

topol.top:
#include "oplsaa.ff/forcefield.itp"
#include "oplsaa.ff/tip5p.itp"

[ system ]
water

[ molecules ]
SOL   512

commands:
editconf -f tip5p.gro -o protein-PBC.gro -bt cubic -d 1.0
genbox -cp protein-PBC.gro -cs tip5p.gro -p topol.top -o protein-water.gro

topol.top after genbox command:
#include "oplsaa.ff/forcefield.itp"
#include "oplsaa.ff/tip5p.itp"

[ system ]
water

[ molecules ]

grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o
protein-water.tpr
Fatal error:
No molecules were defined in the system

There isnt the number of water molecules in topol.top after genbox command.
I dont understand why they have been deleted.




2013/4/11 Justin Lemkul <jalemkul at vt.edu>

> On Thu, Apr 11, 2013 at 9:27 AM, Ahmet yıldırım <ahmedo047 at gmail.com>
> wrote:
>
> > I am simulating tip5p water. I got tip5p.gro from $GMXLIB
> > 1.) editconf -f tip5p.gro -o protein.pdb
> > 2.) pdb2gmx -f protein.pdb -o protein.gro -p protein.top
> >
> > 14 (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals))
> >
> > Select the Water Model:
> >  1: TIP4P  TIP 4-point, recommended
> >  2: TIP3P  TIP 3-point
> >  3: TIP5P  TIP 5-point
> >  4: SPC    simple point charge
> >  5: SPC/E  extended simple point charge
> >  6: None
> >
> > 3 (TIP5P  TIP 5-point)
> >
> > 3.) editconf -f protein.gro -o protein-PBC.gro -bt cubic -d 1.0
> > 4.) genbox -cp protein-PBC.gro -cs tip5p.gro -p protein.top -o
> > protein-water.gro
> > 5.) grompp -v -f minim.mdp -c protein-water.gro -p protein.top -o
> > protein-water.tpr
> > Fatal error:
> > number of coordinates in coordinate file (protein-water.gro, 37090)
> >              does not match topology (protein.top, 34530)
> >
> >
> >
> What does the [molecules] directive of your .top say? In principle, most of
> the steps carried out above are unnecessary. You've got pure water, so the
> topology is easy:
>
> #include "oplsaa.ff/forcefield.itp"
> #include "oplsaa.ff/tip5p.itp"
>
> [ system ]
> water
>
> [ molecules ]
> SOL   X
>
> ...where X is the number of water molecules.
>
> -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