[gmx-users] Regarding ffG43a1p force field
Ramachandran G
gtrama at gmail.com
Thu Jun 23 09:29:41 CEST 2011
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.
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