[gmx-users] defining impropers necessary?

[gromacs query]

>>what you mean here about the improper being defined "about bonds."

Sorry I meant peptide bond itself

>> That's all there is to it.

Does that mean Yes and I understood it correctly or something else? sorry
about that!

regards,
Jiom


On Wed, Jul 17, 2013 at 9:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 <jalemkul at outerbanks.umaryland.edu>> | (410)
>>> 706-7441
>>>
>>> ==============================****====================
>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before
>>> posting!
>>>
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>> >
>>>
>>>
> --
> ==============================**====================
>
> 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
>
> ==============================**====================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>