New problem during processing of y structure via GROMPP ERROR 217 [file topol.top, line 34183]: No default Improper Dih. types
ERROR 218 [file topol.top, line 34184]: No default Improper Dih. types ERROR 219 [file topol.top, line 34185]: No default Improper Dih. types ERROR 220 [file topol.top, line 34186]: No default Improper Dih. types ERROR 221 [file topol.top, line 34187]: No default Improper Dih. types ------------------------------------------------------- Fatal error: Unknown cmap torsion between atoms 915 917 919 934 946 1) Does the errors about Improper types due to non-standart atom names in the RTP? Must I use only standard charmm atom names in that section ? ( I've used Swiss Param's abbreviation see below) [ 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 2 ) In the fatal error the 915 917 919 93 atoms is the C atom of i-2 N Cb C atoms of i-1 and N of the i-residue where i is the chromophore. In the RTP file I notice that CMAP for standard amino acids is the from N to C end of the corresponded and\or adjacent residues. How I could define it for my chromophore composed from 3 residues-like objects ? Should something like below example work ? Also I didnt observe such CMAP for HEME molecule. [ cmap ] -C N CA1 C1 N3 C1 N3 CA3 C +N In tht exmple -C and +N atoms of adjacent residues and others atoms are from chromophore. James 2012/12/12, James Starlight <jmsstarli...@gmail.com>: > 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? 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