[gmx-users] Regarding ffG43a1p force field
bharat gupta
bharat.85.monu at gmail.com
Thu Jun 23 09:49:13 CEST 2011
i will try ... and will reply pack to u
On Thu, Jun 23, 2011 at 4:39 PM, Ramachandran G <gtrama at gmail.com> wrote:
> 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.
>>>>>
>>>>> --
>>>>> 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
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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
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Postdoctoral Research Scholar,
> Department of Chemistry,
> University of Nevada, Reno.
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
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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