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 <[email protected]> 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.
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