Justin, The IMPROPERS consisted of atom names (its correct as I understood). The bond tern I've changed. The resulted RTP
[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 N NC=O -0.7301 6 CA1 CR 0.3611 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 O3 O=C -0.5700 15 CA2 C=C 0.1854 16 CA3 CR 0.3611 17 C C=O 0.5690 18 O O=C -0.5700 19 CB2 C=C -0.1784 20 OH OR -0.5325 21 HA1 HCMM 0.0000 22 HA32 HCMM 0.0000 23 HA33 HCMM 0.0000 24 HD1 HCMM 0.1500 25 HD2 HCMM 0.1500 26 HE1 HCMM 0.1500 27 HE2 HCMM 0.1500 28 HG11 HCMM 0.0000 29 HG12 HCMM 0.0000 30 HG13 HCMM 0.0000 31 HOG1 HOR 0.4000 32 HB2 HCMM 0.1500 33 H11 HNCO 0.3700 34 HH HOCC 0.4500 35 HB1 HCMM 0.0000 36 [ bonds ] HG11 CG1 HG12 CG1 CG1 HG13 CG1 CB1 OG1 HOG1 OG1 CB1 CB1 HB1 CB1 CA1 HE2 CE2 N H11 N CA1 HH OH CA1 HA1 CA1 C1 CE2 CD2 CE2 CZ HD2 CD2 OH CZ CD2 CG2 CZ CE1 N2 C1 N2 CA2 C1 N3 HA33 CA3 CG2 CB2 CG2 CD1 CE1 HE1 CE1 CD1 CA2 CB2 CA2 C2 N3 CA3 N3 C2 CB2 HB2 CA3 C CA3 HA32 CD1 HD1 C2 O3 C O [ impropers ] CG2 CD1 CB2 CD2 CD1 CE1 CG2 HD1 CD2 CE2 CG2 HD2 CE2 CZ CD2 HE2 CB2 CA2 CG2 HB2 CA2 N2 CB2 C2 C1 CA1 N2 N3 CA1 N C1 CB1 CA1 CB1 C1 HA1 CB1 OG1 CA1 CG1 CB1 CG1 CA1 HB1 C2 N3 CA2 O3 N3 C2 C1 CA3 CA3 C N3 HA33 CA3 HA33 N3 HA32 CZ CE1 CE2 OH CE1 CZ CD1 HE1 CG1 HG11 CB1 HG12 CG1 HG11 CB1 HG13 ; with next residue C +N CA3 O ; with previous residue N -C CA1 H11 That produce correct structure from my eGFP model :) But I suppose that charges should be changed in accordance to the paper which you provide me ( in my case charges were assigned by Swiss Param's building blocks) Thanks for help James 2012/12/12, Justin Lemkul <jalem...@vt.edu>: > > > On 12/12/12 6:54 AM, James Starlight wrote: >> 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 ? >> > > + and - indicate next and previous residues, respectively. Presumably your > > chromophore engages in the same types of peptide bonds as any other amino > acid, > so the syntax is the same as any other case. > > -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
