>>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 <jalem...@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 <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 <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> >>> <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-requ...@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@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? 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