[gmx-users] Regarding ffG43a1p force field
bharat gupta
bharat.85.monu at gmail.com
Thu Jun 23 09:26:47 CEST 2011
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
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110623/016e8874/attachment.html>
More information about the gromacs.org_gmx-users
mailing list