That the mollecule that I made [ CRO ] [ atoms ] CG2 CB 0.0284 0 CD1 CB -0.1500 1 CD2 CB -0.1500 2 CE1 CB -0.1500 3 CE2 CB -0.1500 4 CZ CB 0.0825 5 HL H 0.3600 39 NR NH1 -0.9900 6 CA1 CR 0.3310 7 CB1 CR 0.2800 8 CG1 CR 0.0000 9 OG1 OR -0.6800 10 C1 C=O 0.4490 11 N2 N=C -0.6210 12 N3 NC=O -0.4201 13 C2 C=O 0.6156 14 O2 O=C -0.5700 15 CA2 C=C 0.1854 16 CA3 CR 0.3611 17 C C=O 0.6590 18 O3 O=C -0.5700 19 CB2 C=C -0.1784 20 OH OR -0.5325 21 HA1 HCMM 0.0000 22 HB1 HCMM 0.0000 23 HA32 HCMM 0.0000 24 HA33 HCMM 0.0000 25 HD1 HCMM 0.1500 26 HD2 HCMM 0.1500 27 HE1 HCMM 0.1500 28 HE2 HCMM 0.1500 29 HH HOCC 0.4500 30 HG11 HCMM 0.0000 31 HG12 HCMM 0.0000 32 HG13 HCMM 0.0000 33 HOG1 HOR 0.4000 34 HB2 HCMM 0.1500 35 OH OR -0.6500 36 H1 HOCO 0.5000 37
[ bonds ] HCMM CR CR CR OR HOR OR CR HCMM CB HL NR NH1 CR HOCC OR CR C=O CB CB OR CB N=C C=O N=C C=C C=O NC=O CB C=C C=C C=C C=C C=O NC=O CR HOCO OR C=C HCMM OR C=O C=O O=C [ impropers ] CG2 CD1 CB2 CD2 CD1 CE1 CG2 HD1 CD2 CE2 CG2 HD2 CE2 CZ CD2 HE2 CB2 CA2 CG2 HB2 CA2 C2 CB2 N2 C1 CA1 N2 N3 CA1 CB1 C1 NR CA1 CB1 C1 HA1 CB1 OG1 CA1 CG1 CB1 CG1 CA1 HB1 C2 N3 CA2 O2 N3 C2 C1 CA3 CA3 C N3 HA33 CA3 HA33 N3 HA32 C OH CA3 O3 CZ CE1 CE2 OH CE1 CZ CD1 HE1 NR C1 CA1 HL CRO 14 3 4 HG1 CG1 CB1 CA1 1 5 HB1 CB1 CA1 OG1 CG1 1 2 HOG1 OG1 CB1 CA1 1 5 HA1 CA1 NR C1 CB1 1 2 H1 OH C O3 1 1 HL NR C1 CA1 1 6 HA32 CA3 C N3 1 6 HA33 CA3 C N3 1 1 HB2 CB2 CG2 CA2 1 1 HD1 CD1 CG2 CE1 1 1 HD2 CD2 CG2 CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ 1 2 HH OH CZ CE1 The only proble which I've forced with is in the N-term and non-integer charge ( 0.290). James 2012/12/11, Justin Lemkul <jalem...@vt.edu>: > > > On 12/11/12 4:13 PM, James Starlight wrote: >> Today I've made parametrization of the chromophore group by means of >> Swiss param and integrated that topology into charmm27 ff. The only >> problem that I have is with the N-term N atom of the chromophore. It's >> likely that I made mistake to parametrize it into full protonated form >> (NH2). >> > > Protonation states of termini can indeed cause problems. Model compounds > often > use capping groups (methyl, acetyl, etc) to mitigate these effects. You can > > probably get some tips from http://pubs.acs.org/doi/abs/10.1021/jp014476w, > or > otherwise just use their parameters. > >> When I've used pdb2gmx on the GFP structure the peptide bond between >> that N atom and adjacent O ( from C term of adjacent residue) is >> incorrect ( both oxygens preserves on the C atom so my system had >> divided onto 2 chains as well as had incorrect charge). How I could >> define the N atom in the topology as the N-terminal? (I've delited >> both hydrogens from RTP as well as from HDB files but the problem >> didn’t resolved. Also I'm using -ignh on the input pdb to ignore all >> hydrogens from the model) >> > > Copying and pasting your .rtp and .hdb entries would help. Also note that > the > chromophore needs to be defined as protein in residuetypes.dat, otherwise > the > protein chain will terminate erroneously and you'll get protonation state > problems. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
