[gmx-users] defining impropers necessary?

[gromacs query]

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.

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


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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