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

Justin Lemkul jalemkul at vt.edu
Tue Sep 18 00:54:25 CEST 2018

On 9/17/18 6:42 PM, Min Wu wrote:
> 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.

VMD is simply guessing the secondary structure wrong. pdb2gmx does not 
change coordinates, but conversion from .pdb to .gro does sacrifice one 
decimal point of precision, which can cause VMD to screw up secondary 
structure rendering. It's functionally meaningless, and since you're 
going to do a simulation anyway, the structure will change somewhat.



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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