[gmx-users] atomtype OV not found

Justin Lemkul jalemkul at vt.edu
Tue Nov 13 01:03:11 CET 2018

On 11/12/18 8:41 AM, Farial Tavakoli wrote:
> Dear Mark
> I changed the way of topology generating in AMBER. The peptidic ligand (has
> 2 phosphotyrosine residues) topology was generated using amber. all of the
> files that I have in my working directory are, Leaprc.ff99SB,
> Learc.phosaa10,  frcmod.phosaa10,  ligand.inpcrd,  ligand.prmtop.  The only
> thing that I know to convert amber format to gromacs format is to use
> acpype python script :
> python acpype -p ligand.prmtop -x ligand.inpcrd
> The .gro and .top files were generated. protein topology was generated
> using amber99SB ff in gromacs and then complex.gro and .top files were
> modified according to the tutorial in gromacs. But now, when I issue this
> command:
> gmx grompp -f .mdp -c .gro -p .top -o ions.tpr
> I face to this error:
> ERROR 1 [file mig_GMX.itp, line 60]:
>    Atomtype OV not found
> OV atom is related to leaprc.phosaa10 file and I dont know what should I do
> now?
> I think , the leaprc.phosaa10 file has to be added to aminoacid.rtp file of
> amber99SB.ff but I dont know how to convert it to gromacs format file?
> Am I right?
> WOuld you please guide me how to remove this Error?

Your force field has to account for all the atom types required to run 
the simulation. You don't need to modify any .rtp files if you've 
already got a topology produced by other means. But that topology should 
be edited to introduce any new atom types required, associated bonded 
parameters, etc. When you do nonstandard things, you have to take 
nonstandard approaches...



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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