When I convert attached .pdb file to .gro using:
pdb2gmx -quiet -ff amber99 -water none -f ${MOL}.pdb -o ${MOL}Initial.gro
-i ${MOL}.itp -p ${MOL}.top -ignh
the generated .gro file causes vmd (1.9.1) to show this warning while
loading it:
Warning) Unusual bond between residues: 905 (protein) and 906 (none)
Should I wonder about it? Or is pdb2gmx (from gromacs 4.6.2) generating a
wrong .gro file for some reason?
Thanks
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