[gmx-users] Re: Fatal error: Atomtype O2 not found

[Justin A. Lemkul]

On 6/11/12 9:54 AM, ramaraju801 wrote:
> hi
> sorry 4 not doing it before, right now am doing  "Solvate the Box"  step in
> molecular modelling  am using Gromacs 4.5.5 ver
>
> during the first step i.e "creating the topology file ",i tried to create
> the topology file by using the command
> "pdb2gmx –ignh –ff G43a1 –f 1OMB.pdb –o fws.pdb –p fws.top" for which
> gromacs showed me an error saying
> "atomtypeXX not found in the residue type database " i resolved this issue
> by going through gromacs manual by adding the missing atoms to the dna.rtp
> file and new atoms to atomtypes.atp file after which it produced the
> topology file
>
> int he next step i setup an box with the command "editconf -bt cubic –f
> fws.pdb –o fws.pdb -c –d 0.9"
>
> in the third step i.e "Solvate the Box" i used the command "genbox –cp
> fws.pdb –cs spc216.gro –o fws_b4em.pdb –p fws.top"
>
>   in the fourth step i.e "Setup the energy minimization." i used the command
> "grompp –f em.mdp –c fws_ion.pdb –p fws.top –o fws_em.tpr"  where its
> givving me an errror which says "Fatal error:
> Unknown bond_atomtype O2"
>

These are presumably commands from a tutorial, which is not what you're working 
on.  The 1OMB.pdb file contains only protein, and the Gromos96 43a1 force field 
does not have DNA parameters, so this workflow is irrelevant.  What you should 
provide is precisely what you are typing for your system, not the tutorial.  We 
know the tutorial works; it's your system that doesn't work.

> based on your replies i tried by adding the atom to ffbonded.itp file but it
> dint work.
>
> am attachning my dna.rtp ,atomtypes.atp,ffbonded .itp files please help
>
> -ram http://gromacs.5086.n6.nabble.com/file/n4998335/dna.rtp dna.rtp

I don't know what you changed here.  Please tell us the change(s) you made.

> http://gromacs.5086.n6.nabble.com/file/n4998335/ffbonded.itp ffbonded.itp

The O2-N3 bond parameters you added are nonsense.  They specify a 1-nm bond with 
a 1-kJ/(mol nm^2) force constant.  If you're just hacking away at these files 
hoping that the workflow will complete without error, then you're wasting your 
time because the dynamics will be nonsense.

-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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