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

[Justin Lemkul]

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

-- 

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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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