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

[Ahmet yıldırım]

I did as you said. I corrected number of water molecules in the topology by
hand.

grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o
protein-water.tpr
Steepest Descents converged to Fmax < 1000 in 3 steps
Potential Energy  = -1.5700267e+05
Maximum force     =  7.2195142e+02 on atom 3761
Norm of force     =  1.3341200e+02

I think these results isnt normal. isnt it?


2013/4/15 Justin Lemkul <jalemkul at vt.edu>

>
>
> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Ahmet Yıldırım