On Thu, Dec 12, 2013 at 12:45 PM, Ehsan Sadeghi <es...@sfu.ca> wrote:
> Hi gmx users, > > I try to use OPLS force field for my simulation. I added the following > residue to the aminoacids.rtp, but when I generate the topol.top file it > does not show the the bond stretching, angle bond, dihedrals. > > > [ NAF ] > [ atoms ] > C1 opls_966 0.3846 1 > C2 opls_966 0.3846 1 > C3 opls_966 0.3846 1 > C4 opls_966 0.3846 1 > F17 opls_972 -0.1923 1 > F18 opls_972 -0.1923 1 > F19 opls_972 -0.1923 1 > F20 opls_972 -0.1923 1 > F21 opls_972 -0.1923 1 > F22 opls_972 -0.1923 1 > F23 opls_972 -0.1923 1 > F24 opls_972 -0.1923 1 > C5 opls_966 0.3846 1 > C6 opls_966 0.3846 1 > C7 opls_966 0.3846 1 > C8 opls_966 0.3846 1 > F25 opls_972 -0.1923 1 > F26 opls_972 -0.1923 1 > F27 opls_972 -0.1923 1 > F28 opls_972 -0.1923 1 > F29 opls_972 -0.1923 1 > F30 opls_972 -0.1923 1 > F31 opls_972 -0.1923 1 > F32 opls_972 -0.1923 1 > C9 opls_966 0.3846 1 > C10 opls_966 0.3846 1 > C11 opls_966 0.3846 1 > C12 opls_966 0.3846 1 > F33 opls_972 -0.1923 1 > F34 opls_972 -0.1923 1 > F35 opls_972 -0.1923 1 > F36 opls_972 -0.1923 1 > F37 opls_972 -0.1923 1 > F38 opls_972 -0.1923 1 > F39 opls_972 -0.1923 1 > F40 opls_972 -0.1923 1 > C13 opls_966 0.3846 1 > C14 opls_966 0.3846 1 > C15 opls_967 0.3218 1 > C16 opls_966 0.3846 1 > F41 opls_972 -0.1923 1 > F42 opls_972 -0.1923 1 > F43 opls_972 -0.1923 1 > F44 opls_972 -0.1923 1 > F45 opls_973 -0.1641 1 > F46 opls_972 -0.1923 1 > F47 opls_972 -0.1923 1 > C48 opls_968 0.3228 1 > O49 opls_980 -0.2742 1 > C50 opls_969 0.401 1 > O51 opls_981 -0.2604 1 > C52 opls_967 0.3218 1 > C53 opls_971 0.3216 1 > F55 opls_974 -0.1637 1 > F56 opls_974 -0.1637 1 > F57 opls_975 -0.1932 1 > C58 opls_970 0.4947 1 > F59 opls_977 -0.1662 1 > F60 opls_977 -0.1662 1 > F61 opls_978 -0.3278 1 > F62 opls_978 -0.3278 1 > F66 opls_976 -0.1649 1 > F67 opls_976 -0.1649 1 > F68 opls_976 -0.1649 1 > S54 opls_979 1.4124 1 > O63 opls_982 -0.632 1 > O64 opls_982 -0.632 1 > O65 opls_982 -0.632 1 > Note that assigning all atoms to a single charge group is inappropriate. Surely grompp will warn about this, but you should construct the groups more carefully. <snip> ---------------- > However, the parameters that we had in topol file are different: > > [ bonds ] > ; ai aj funct c0 c1 c2 c3 > 1 2 1 > 1 5 1 > > [ angles ] > ; ai aj ak funct c0 c1 c2 > c3 > 2 1 5 1 > 2 1 6 1 > 5 1 6 1 > -------------------------------- > > How gromacs can find c0, c1,c2 and c3 from b0, kb, th0, and cth in the > ffbonded.itp? > > I answered this already: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-December/086118.html You provide the parameters in ffbonded.itp, grompp goes and finds them. If something is missing, grompp fails. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ========================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
