[gmx-users] Regarding ffG43a1p force field
Ramachandran G
gtrama at gmail.com
Thu Jun 23 09:39:30 CEST 2011
It is neutral.
I tried sending the coordinates but it bounces. So i paste below the
chromophore coordinates alone.
64CRIH CB2 948 2.946 2.849 3.832
64CRIH HB2 949 2.948 2.845 3.932
64CRIH CA2 950 2.827 2.790 3.770
64CRIH N2 951 2.795 2.778 3.639
64CRIH C1 952 2.683 2.711 3.636
64CRIH N3 953 2.629 2.694 3.756
64CRIH C2 954 2.723 2.736 3.850
64CRIH OC2 955 2.694 2.757 3.968
64CRIH CG2 956 3.059 2.911 3.774
64CRIH CZ 957 3.282 3.042 3.676
64CRIH CD1 958 3.085 2.912 3.634
64CRIH HD1 959 3.023 2.867 3.569
64CRIH CD2 960 3.152 2.973 3.862
64CRIH HD2 961 3.143 2.961 3.961
64CRIH CE1 962 3.198 2.975 3.589
64CRIH HE1 963 3.220 2.974 3.492
64CRIH CE2 964 3.253 3.048 3.811
64CRIH HE2 965 3.307 3.108 3.871
64CRIH OH 966 3.391 3.101 3.633
64CRIH HH 967 3.439 3.143 3.710
64CRIH N 968 2.533 2.768 3.461
64CRIH H 969 2.581 2.856 3.437
64CRIH CA1 970 2.614 2.661 3.514
64CRIH CB1 971 2.714 2.610 3.411
64CRIH OG1 972 2.778 2.493 3.461
64CRIH HG1 973 2.875 2.504 3.442
64CRIH CA3 974 2.494 2.655 3.788
64CRIH C 975 2.491 2.532 3.876
64CRIH O 976 2.414 2.527 3.972
On Thu, Jun 23, 2011 at 12:34 AM, bharat gupta <bharat.85.monu at gmail.com>wrote:
> Is is this for the neutral chromophore or protonated one ??
>
>
> On Thu, Jun 23, 2011 at 4:29 PM, Ramachandran G <gtrama at gmail.com> wrote:
>
>> yes!
>>
>>
>> On Thu, Jun 23, 2011 at 12:26 AM, bharat gupta <bharat.85.monu at gmail.com>wrote:
>>
>>> these are in continuity I mean for the ffbonded.itp file
>>>
>>> On Thu, Jun 23, 2011 at 4:21 PM, Ramachandran G <gtrama at gmail.com>wrote:
>>>
>>>> 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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>>>
>>>
>>>
>>> --
>>> Bharat
>>> Ph.D. Candidate
>>> Room No. : 7202A, 2nd Floor
>>> Biomolecular Engineering Laboratory
>>> Division of Chemical Engineering and Polymer Science
>>> Pusan National University
>>> Busan -609735
>>> South Korea
>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>> Mobile no. - 010-5818-3680
>>> E-mail : monu46010 at yahoo.com
>>>
>>>
>>> --
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>>
>>
>>
>> --
>> Postdoctoral Research Scholar,
>> Department of Chemistry,
>> University of Nevada, Reno.
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>
--
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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