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

[Justin Lemkul]

On 4/15/13 6:58 AM, Ahmet yıldırım wrote:
> 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.
>

I cannot reproduce this problem with version 4.6, but it's trivial to just add 
the correct number of water molecules in the topology by hand.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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