Is is this for the neutral chromophore or protonated one ?? On Thu, Jun 23, 2011 at 4:29 PM, Ramachandran G <[email protected]> wrote:
> yes! > > > On Thu, Jun 23, 2011 at 12:26 AM, bharat gupta > <[email protected]>wrote: > >> these are in continuity I mean for the ffbonded.itp file >> >> On Thu, Jun 23, 2011 at 4:21 PM, Ramachandran G <[email protected]> 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 <[email protected]>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 <[email protected]>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 [email protected] >>> 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 [email protected]. >>> 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 : [email protected] >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> 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 [email protected] > 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 [email protected]. > 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 : [email protected]
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
