Oh that problem was imperically resolved by renamind O2 ( which are not terminal but pdb2gmx define them as a terminal ) atom to O3
The only question about my chromophore is the definition of the IMPROPER groups. As I've posted above my initial model was CAPPED from C and N termi by NH2 and Ace. The resulted topology consisted of Improper for bonds between chromophore atoms and Capped groups ( e.g : With ACE (C-3 O-1 C-4 H-11 H-12 H-1 ) IMPH C N1 CA3 O IMPH N C3 CA1 H11 IMPH C3 O1 N C4 IMPH C4 HC11 C3 H1 IMPH C4 HC11 C3 H12 With NH2 (N1-H2-H3) IMPH N1 H2 C H3 IMPH C N1 CA3 O That strings were removed from chromophore RTP. But in my final model there are 2 amino acids insted of capped groups so the IPROPERS must be inclusion for protein-chromophore nonds. How it could be done ? In some amino acids I've found -N and -C blocks that (if I understood correctly) for C and N atoms of the adjacent residues. How that atoms must be defined correctly in the protein-chromophore comples ? James James 2012/12/12, James Starlight <jmsstarli...@gmail.com>: > Also I've made the same parameters with the capped chromophore (NH2 on > the C-term (instead of OH) and ACE on the N term (instead of H). > > When I've defined that chromophore as the Protein I've obtained an error > > Fatal error: > Atom OXT in residue CRO 66 was not found in rtp entry CRO with 38 atoms > while sorting atoms > > I've not found any OXT atoms in the residues in the RTP of other amino > acids. Must that terminal oxygen be missing OH ( which I've replaced > my ACE in my model) ? Where it should be defined ? > > James > > > 2012/12/11, James Starlight <jmsstarli...@gmail.com>: >> 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. 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