[gmx-users] defining impropers necessary?

[Justin Lemkul]

On 7/17/13 1:33 PM, gromacs query wrote:
> Dear Justin,
>
> Thanks for reply and explanation, and..:
>
>>> you've got an amide flanked by two methylene groups as the repeat unit
>>> All the amino acids in the aminoacids.rtp file specify impropers
> centered on the C and N atoms of the peptide bond.
>
> I meant to say its easy to define (in general) impropers for chiral
> centers, but not sure about bonds (here peptide). In oplsaa.ff I just
> looked ALA in aminoacids.rtp for which there are two impropers.
>

I don't know what you mean here about the improper being defined "about bonds." 
  You're defining a central atom, around which there are 3 atoms that define the 
planarity of the central atom.  Basically, any sp2 center can be defined in this 
way.

> ALA impropers:
>
>    -C    CA     N     H    improper_Z_N_X_Y
>      CA    +N     C     O    improper_O_C_X_Y
>
> which should be as follows:
>
>                H   CH3        H
>                 I    I              I
> (-)C---------N--CA--C-------N(+)
>      I               I     I
>     O              H   O
>     ^              ^             ^
>     ^              ^             ^
>   [-C]---------[ALA]-------[N+]
>
>
> Does this mean both improper terms are making peptide bond planar (two
> peptide bonds: left side and right side of ALA), but in my case as you
> noticed there are two methylene groups. So is it correct if I define
> improper for my polymer as:
>
> C   C2  N   H
> C1  N   C   O
>

That's all there is to it.

-Justin

>
> thanks
>
> regards,
> Jiom
>
>
> On Wed, Jul 17, 2013 at 6:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/17/13 11:39 AM, gromacs query wrote:
>>
>>> Dear Justin,
>>>
>>> 1) I can understand the improper for stereocenters (chiral) easily but
>>> with
>>>
>>
>> OPLS doesn't use impropers for chiral centers.
>>
>>
>>   bonds I am confused (I have tried to explain below please let me know if I
>>> have defined impropers correctly for peptide to keep it planar).
>>>
>>>    H1     O          H3
>>>       \      I          /
>>>    --C1---C--N---C2--
>>>       /         I      \
>>>     H2       H      H4
>>>
>>>
>>>
>> OK, funky text drawing :)  But it looks like you've got an amide flanked
>> by two methylene groups as the repeat unit.
>>
>>
>>   So I think improper (being zero) to keep peptide planar should be defined
>>> (and sufficiently) as: O C N C1
>>> and dihedral should be which is simple as: O C N H
>>>
>>> But it confuses me, why one needs to define improper for peptide. If I
>>> just
>>> keep dihedral angle strict (high force constant) then it will make peptide
>>> freezed! so it will remain planar.
>>>
>>>
>> The OPLS approach for amides is to define normal dihedrals as well as
>> impropers.  Keep in mind that rotations about a bond and out-of-plane
>> bending are different types of motion.  I suppose you could achieve what
>> you're thinking of by very strong force constants for the dihedrals, but I
>> would wonder if you're then throwing the balance of 1-4 interactions
>> (especially charges) out of whack.
>>
>>
>>   2) Also, I am not sure whether OPLS needs this peptide bond to be defined
>>> with improper, someone have experienced this please suggest?
>>>
>>>
>> All the amino acids in the aminoacids.rtp file specify impropers centered
>> on the C and N atoms of the peptide bond.  I would stick with that approach.
>>
>>
>> -Justin
>>
>> --
>> ==============================**====================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
>> 706-7441
>>
>> ==============================**====================
>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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