You can also look them up (angles bond distances) in the CRC handbook or online and just put the angle(distances direct into the .itp file for your ligand, as well as impropers...it works for all the force fields, unless you use hybrids (CH3=1 representation)...it comes out wierd as the different force fields put the same numbers different. Such as distance 1.18, 118.0 to 11800000.0 depending on representation is all...
Stephan
Gesendet: Mittwoch, 17. Juli 2013 um 19:33 Uhr
Von: "gromacs query" <gromacsqu...@gmail.com>
An: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: Re: [gmx-users] defining impropers necessary?
Von: "gromacs query" <gromacsqu...@gmail.com>
An: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: Re: [gmx-users] defining impropers necessary?
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> | (410)
> 706-7441
>
> ==============================**====================
> --
> gmx-users mailing list gmx-users@gromacs.org
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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> | (410)
> 706-7441
>
> ==============================**====================
> --
> gmx-users mailing list gmx-users@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-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
--
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