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

MD refmac5 at gmail.com
Wed Jan 17 15:40:40 CET 2018

​Hi! You are completely right about the parametrization. I found the
pyrodoxal in charmm and I think I am going to start over to combine it with
lys which can reduce input from outside source to make charmm happy.
however I left the md.mdp run yesterday and this morning i found the methyl
group is fixed, the ring went back to flat... not quite sure what happened
between minimization and simulation.  ​but yes I wouldn't really trust the
results based on the discrepancies. Thanks for the advice :)


On Tue, Jan 16, 2018 at 7:37 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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