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
