more parameters - ffbonded.itp NB CT 1 0.1444 294553.6 NB C 1 0.1404 334720.0 C CC 1 0.1407 343088.0 CC CB 1 0.1474 468608.0 CB H2 1 0.1076 129960.25
to aminoacids.hdb 1 1 HE2 CE2 CZ CD2 1 1 HE1 CE1 CZ CD1 1 1 HD1 CD1 CG2 CE1 1 1 HD2 CD2 CG2 CE2 1 2 HH OH CZ CE1 1 1 HB2 CB2 CA2 CG2 1 2 HG1 OG1 CB1 CA1 1 1 H N CA1 C1 On Thu, Jun 23, 2011 at 12:18 AM, Ramachandran G <gtr...@gmail.com> wrote: > For ffbonded.itp, i added the following. (you need to be carefull here > since i cooked upto the force constants) > C CC CB CA 9 180.0 4.309 1 > NB CC C O 9 180.0 4.309 1 ; > NB CC CB CA 9 180.0 4.309 1 > NB CC CB H2 9 180.0 4.309 1 > C CC CB H2 9 180.0 4.309 1 > NB CC C NB 9 180.0 4.0876 1 > CT NB C CC 9 180.0 4.0876 1 > CT NB C O 9 180.0 4.0876 1 > CB CC C NB 9 180.0 4.0876 1 > CB CC C O 9 180.0 4.0876 1 > CC C NB CC 9 180.0 4.7656 1 > O C NB CC 9 180.0 4.7656 1; > CC NB CT C 9 180.0 4.1400 1; > C NB CT C 9 180.0 4.1400 1 ; > CT CT OH HO 4 180.0 4.1400 1 ; > OH CT CT CC 9 0.0 4.1400 1 > OH CT CT N 9 180.0 4.9162 1 > > ; added newly improper dihedrals > CB CC CA H2 4 180.0 4.1840 2 > CC NB CB C 4 180.0 4.1840 2 > CC CT NB NB 4 180.0 4.1840 2 > CT N CC CT 4 144.64 3.1840 2 > NB O CC C 4 180.0 4.1840 2 > NB CC C CT 4 180.0 4.1840 2 > CA CB CA CA 4 180.0 4.1840 2 > CA HA CA CA 4 180.0 4.1840 2 > ; added to test > N CT C H 4 180.0 4.1840 2 > > > > > On Thu, Jun 23, 2011 at 12:13 AM, Ramachandran G <gtr...@gmail.com> wrote: > >> For the GFP chromophore i name residue as CRIH. >> 1. aminoacids.rtp >> CB2 CB 0.019103 1 >> CA2 CC -0.026635 2 >> N2 NB -0.436463 3 >> C1 CC 0.302706 4 >> N3 NB -0.541478 5 >> C2 C 0.563844 6 >> OC2 O -0.394118 7 >> CG2 CA -0.079330 8 >> CZ CA 0.240178 9 >> CD1 CA -0.072596 10 >> HD1 HA 0.129374 11 >> CD2 CA -0.070677 12 >> HD2 HA 0.091532 13 >> CE1 CA -0.129374 14 >> HE1 HA 0.091792 15 >> CE2 CA -0.087778 16 >> HE2 HA 0.112301 17 >> OH OH -0.454413 18 >> H H 0.37107 19 >> HH HO 0.258435 20 >> N N -0.61682 21 >> CA1 CT -0.116631 22 >> CB1 CT -0.03127 23 >> OG1 OH -0.74662 24 >> HG1 HO 0.45887 25 >> HB2 H2 0.116716 26 >> CA3 CT -0.250251 27 >> C C 0.35254 28 >> O O -0.48366 29 >> [ bonds ] >> C1 CA1 >> N3 CA3 >> N3 C1 >> N3 C2 >> C2 OC2 >> C1 N2 >> C2 CA2 >> N2 CA2 >> CA2 CB2 >> CB2 CG2 >> CG2 CD1 >> CG2 CD2 >> CD1 CE1 >> CD2 CE2 >> CE1 CZ >> CE2 CZ >> CZ OH >> CB1 OG1 >> OH HH >> CB2 HB2 >> CD1 HD1 >> CD2 HD2 >> CE1 HE1 >> CE2 HE2 >> CA1 N >> CA1 CB1 >> CA3 C >> C O >> OG1 CB1 >> OG1 HG1 >> N H >> -C N >> +N C >> [ angles ] >> ; ai aj ak th0 cth ub0 cub >> N2 C1 N3 114.0 1087.87 >> C1 N2 CA2 106.0 1087.87 >> C1 N3 C2 107.9 1087.87 >> N2 CA2 C2 108.3 1087.87 >> N2 CA2 CB2 129.5 376.56 >> C2 N3 CA3 123.4 267.776 >> N3 C2 OC2 126.0 351.456 >> N3 C2 CA2 103.0 1087.87 >> OC2 C2 CA2 132.0 317.984 >> C2 CA2 CB2 122.0 376.56 >> CA2 CB2 CG2 130.0 1087.87 >> CB2 CG2 CD1 121.0 383.2544 >> CB2 CG2 CD2 121.0 383.2544 >> CG2 CD1 CE1 120.0 334.72 >> CG2 CD2 CE2 120.0 334.72 >> CD1 CG2 CD2 120.0 334.72 >> CD1 CE1 CZ 120.0 334.72 >> CD2 CE2 CZ 120.0 334.72 >> CE1 CZ CE2 120.0 334.72 >> OH CZ CE1 120.0 378.2336 >> OH CZ CE2 120.0 378.2336 >> HH OH CZ 108.0 543.92 >> HG1 OG1 CB1 108.0 543.92 >> N2 C1 CA1 125.0 334.72 >> N3 C1 CA1 121.4 292.88 >> C1 N3 CA3 129.0 301.248 >> HB2 CB2 CA2 114.0 351.456 >> HB2 CB2 CG2 116.0 351.456 >> HD1 CD1 CG2 120.0 251.04 >> HD1 CD1 CE1 120.0 251.04 >> HD2 CD2 CG2 120.0 251.04 >> HD2 CD2 CE2 120.0 251.04 >> HE1 CE1 CZ 120.0 251.04 >> HE1 CE1 CD1 120.0 251.04 >> HE2 CE2 CZ 120.0 251.04 >> HE2 CE2 CD2 120.0 251.04 >> CA1 N H 118.4 317.984 >> CA1 CB1 OG1 109.5 669.44 >> N CA1 CB1 109.7 669.44 >> CB1 CA1 C1 111.1 527.184 >> CA3 C O 120.4 669.44 >> N CA1 C1 110.1 527.184 >> C CA3 N3 110.3 669.44 >> CA3 C N 116.6 585.76 >> C2 CA2 CB2 CG2 ; >> N2 CA2 CB2 CG2 >> CA2 CB2 CG2 CD1 ; >> CA2 CB2 CG2 CD2 ; >> N2 CA2 CB2 HB2 >> C2 CA2 CB2 HB2 >> HB2 CB2 CG2 CD1 ; >> HB2 CB2 CG2 CD2 ; >> CB2 CG2 CD1 CE1 ; >> CB2 CG2 CD2 CE2 ; >> CD1 CE1 CZ CE2 >> CD1 CE1 CZ OH >> CE1 CZ OH HH >> CE2 CZ OH HH >> CG2 CD1 CE1 CZ >> HD1 CD1 CG2 CD2 >> HD1 CD1 CE1 CZ >> HD2 CD2 CG2 CD1 >> HD2 CD2 CE2 CZ >> HE1 CE1 CD1 CG2 >> HE1 CE1 CZ CE2 >> HE2 CE2 CD2 CG2 >> HE2 CE2 CZ CE1 >> CA1 C1 N2 CA2 ; >> CA1 C1 N3 C2 ; >> CA3 N3 C2 CA2 >> CA3 N3 C1 N2 ; >> CG2 CB2 CA2 N2 ; repeated >> CG2 CB2 CA2 C2 ; repeated >> CB2 CA2 N2 C1 >> CB2 CA2 C2 N3 >> CA2 N2 C1 N3 >> CA2 C2 N3 C1 >> OG1 CB1 CA1 C1 ; >> OG1 CB1 CA1 N ; >> CA1 CB1 OG1 HG1 ; >> N3 CA3 C O ; >> OC2 C2 CA2 CB2 ; >> OC2 C2 N3 CA3 ; >> OC2 C2 CA2 N2 ; >> OC2 C2 N3 C1 ; >> N3 CA3 C +N ; added to link the neighbouring valine >> CA3 C +N +H ; >> CA3 C +N +CA ; >> CB1 CA1 N -C ; added to link the neighbouring PHE >> C1 CA1 N -C ; >> CA1 N -C -O ; >> H N -C -O ; n >> [ impropers ] >> C1 CA1 N2 N3 >> CA2 N2 CB2 C2 >> C2 CA2 OC2 N3 >> CG2 CB2 CD1 CD2 >> CZ CE1 CE2 OH >> N3 C1 C2 CA3 >> CB2 CA2 CG2 HB2 >> CD1 CG2 HD1 CE1 >> CD2 CG2 HD2 CE2 >> CE1 CD1 HE1 CZ >> CE2 CD2 HE2 CZ >> CA1 N C1 CB1 >> C CA3 N O ; >> N CA1 C H ; >> >> >> >> >> >> > > > -- > Postdoctoral Research Scholar, > Department of Chemistry, > University of Nevada, Reno. > -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno.
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