[gmx-users] helix change to coil for residues His 177 and His 187 after pdb2gmx in opls-aa forcefield

[Min Wu]

Hi All,


When I use pdb2gmx of gromacs 5.0.7 to convert 2lsb.pdb to gro file, the
initial helix structure of His 177 and His 187 change to coil. I modified
the His to HISD  in the original pdb to match the residue name in opls-aa
forcefield.  When I change HISD back to HIS, when viewed in VMD, the helix
is back. But when using pdb2gmx, I always got error information, if I keep
HIS as the residue name.

Do you have any idea what might be the possible problem? Thank you.

Min