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 <jalem...@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@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> |
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> 706-7441
>
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