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.
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