i will try ... and will reply pack to u
On Thu, Jun 23, 2011 at 4:39 PM, Ramachandran G <[email protected]> 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 > <[email protected]>wrote: > >> 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 >> > > > > -- > 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]
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