[gmx-users] Regarding ffG43a1p force field
bharat gupta
bharat.85.monu at gmail.com
Thu Jun 23 09:34:55 CEST 2011
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
>>
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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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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> Please search the archive at
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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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