[gmx-users] Regarding ffG43a1p force field
Ramachandran G
gtrama at gmail.com
Thu Jun 23 09:21:52 CEST 2011
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 <gtrama at 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 <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 ;
>>
>>
>>
>>
>>
>>
>
>
> --
> Postdoctoral Research Scholar,
> Department of Chemistry,
> University of Nevada, Reno.
>
--
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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