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

MD refmac5 at gmail.com
Tue Jan 16 12:39:03 CET 2018


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

Ming

On Mon, Jan 15, 2018 at 7:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/15/18 7:45 PM, MD wrote:
>
>> Hi Gromacs,
>>
>> I have a modified side chain amino acid and it has a six member ring
>> attached to it. Regarding this ring I had dihedral angles taken care with
>> some 0s and some 180s. However, after minimization my structure looks very
>> strange, the ring is not flat and the dihedral angles in my settings
>> didn't
>> seem to apply to the minimized structure at all. Any thoughts?
>>
>
> You're going to have to provide a lot more detail. You're parametrizing
> something nonstandard, so there are plenty of places to make mistakes.
> Without knowing your structure, the actual parameters and how derived and
> validated them, there's nothing to do but guess.
>
> Keep in mind that rings are not necessarily perfectly planar, and the
> values set for dihedral phase offsets do not strictly mean the values that
> the dihedrals must adopt.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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>
> jalemkul at vt.edu | (540) 231-3129
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>
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