[gmx-users] atomtype OV not found
faryal.tavakoli at gmail.com
Mon Nov 12 14:41:48 CET 2018
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
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
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?
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