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

[Justin Lemkul]

On 1/17/18 9:35 AM, MD wrote:
> Hi, so yesterday I left it moving forward to do the md.mdp. Very strangely,
> the ring goes back to flat form after md.mdp. I am not quite sure what
> happened here?

As I said yesterday, the topology you generated was based on incorrect 
structure and inappropriate mixing of atom types. Whatever behavior it 
exhibits is basically due to random chance unless you do the work to 
parametrize it properly. Even if you get some serendipitous outcome, 
don't trust it.

-Justin

> Ming
>
> On Tue, Jan 16, 2018 at 6:43 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> You still have many sources of problems (e.g. the warnings you suppressed,
>> the fact that your ring's atoms interact with an environment). What happens
>> when you minimize a capped peptide in vacuo?
>>
>> Mark
>>
>> On Tue, Jan 16, 2018 at 12:39 PM MD <refmac5 at gmail.com> 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
>>> 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
>>>>
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>>
>>>> ==================================================
>>>>
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-- 
==================================================

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================