[gmx-users] Regarding ffG43a1p force field
Ramachandran G
gtrama at gmail.com
Thu Jun 23 09:18:03 CEST 2011
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 <gtrama at 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 ;
>
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--
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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