[gmx-users] six member ring won't stay flat

Justin Lemkul jalemkul at vt.edu
Tue Jan 16 13:38:02 CET 2018

On 1/16/18 6:38 AM, MD wrote:
> Hi Justin,
> I got the itp and parameters of my side chain modified amino acid from
> CHARMM-GUI and incorporated it into my protein structure, labeled with
> HETATM. I made the atom types names consistent with charmm forcefield which
> I used with gromacs and made sure overall the parameters look decent for
> now. After some fixing the grompp would run with no warnings, and I did a
> quick energy minimization, but ended up with a distorted six member ring. I
> have the picture and my parameters attached. Your time is appreciated :)
> https://docs.google.com/document/d/1bjSq55HDLRsSVGqm5i0MRwI-rgIesxy0QdIHm7tqTug/edit?usp=sharing

You have a number of problems. If that's simply pyridoxal phosphate 
linked with lysine, then you have lots of missing H atoms and the 
protonation state of your phosphate group is incorrect, at least with 
respect to normal physiological pH. You're getting a lot of distortion 
from a lot of places, not the least of which is that you should have a 
methyl group attached to the ring, not a methylene (=CH2), as that 
changes the conjugation entirely.

Also, as I said before - *do not* mix CGenFF and standard CHARMM 
parameters. You can't just change around atom types until grompp 
warnings go away. What you're seeking to do is complicated and requires 
great care, otherwise you get garbage. There's no magic push-button 
here. You've got to do a thorough parametrization, including all the 
things I said before. Anything short of that, in this instance, is 
likely to fail. You can take initial guess charges from existing groups 
in CHARMM, without even going to CGenFF, as most of those groups should 
already be well described.



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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