Hi Elizabeth, These missing terms are filled in automatically by grompp from the bondtypes, angletypes and dihedraltypes definitions in the *bon.itp. Unless grompp complains about missing terms, you'll be fine. You can check whether everything is okay by writing out a processed topology (grompp -pp) and looking up the bonds.angles/dihedrals there.
Cheers, Tsjerk On Wed, Nov 23, 2011 at 12:32 AM, Elizabeth Ploetz <plo...@ksu.edu> wrote: > Greetings Gromacs Users, > > I am building the topology file for a protein with three disulfide bonds > (bovine pancreatic trpysin inhibitor). When using any of the GROMOS FFs the > topol.top output of pdb2gmx has missing bond, angle, and dihedral types on > the lines describing the three disulfides. (The residue names do change > appropriately i.e., CYS becomes CYS2.) The disulfides do form correctly when > using the other currently available FFs. All the output shown below my > message is from running GROMACS-4.5.5. Note the same thing happens when > running GROMACS-4.5.3 and GROMACS-4.0.5. > > I have not found any discussion of this issue on the internet (in general) or > the gmx mailing list (specifically), however I suspect this may have > contributed to at least one user message ( > http://lists.gromacs.org/pipermail/gmx-users/2011-March/059242.html ). It is > trivial to fill in the missing bond, angle, and dihedral types by hand after > running pdb2gmx (this may be why this has not been discussed too much), but I > am interested in figuring out a long term solution because the lab I work in > has developed a FF which uses the GROMOS bonds and angles (and thus also uses > the same format as GROMOS does for the ffbonded.itp file). We hope to have > our FF supported by GROMACS in the future, but we want to make sure that > GROMACS users would not encounter this problem if they selected our FF. > > Could anyone point me in the right direction? > > Thanks for your consideration of this! > > All the best, > > Elizabeth A. Ploetz > Kansas State University > > The list below shows the tested FFs. A '+' indicates proper disulfide > description in the topology file, and an 'X' indicates the output contained > missing bond/angle/dihedral types. > > Test of disulfide bond formation using pdb2gmx and FFs available in > GROMACS-4.5.5: > + 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, > 1999-2012, 2003) > + 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) > + 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, > 461-469, 1996) > + 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, > 1049-1074, 2000) > + 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, > 2006) > + 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., > Proteins 78, 1950-58, 2010) > + 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) > + 8: CHARMM27 all-atom force field (with CMAP) - version 2.0 > X 9: GROMOS96 43a1 force field > X10: GROMOS96 43a2 force field (improved alkane dihedrals) > X11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) > X12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) > X13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) > +14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) > +15: [DEPRECATED] Encad all-atom force field, using full solvent charges > +16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges > +17: [DEPRECATED] Gromacs force field (see manual) > +18: [DEPRECATED] Gromacs force field with hydrogens for NMR > > This is an example of how I ran pdb2gmx: > :-) G R O M A C S (-: > > Gromacs Runs On Most of All Computer Systems > > :-) VERSION 4.5.5 (-: > . > . skipping > . > Select the Force Field: > >From '/usr/local/gromacs/share/gromacs/top': > 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, > 1999-2012, 2003) > 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) > 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, > 461-469, 1996) > 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, > 1049-1074, 2000) > 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, > 2006) > 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins > 78, 1950-58, 2010) > 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) > 8: CHARMM27 all-atom force field (with CMAP) - version 2.0 > 9: GROMOS96 43a1 force field > 10: GROMOS96 43a2 force field (improved alkane dihedrals) > 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) > 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) > 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) > 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) > 15: [DEPRECATED] Encad all-atom force field, using full solvent charges > 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges > 17: [DEPRECATED] Gromacs force field (see manual) > 18: [DEPRECATED] Gromacs force field with hydrogens for NMR > 13 > > Using the Gromos53a6 force field in directory gromos53a6.ff > > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/watermodels.dat > > Select the Water Model: > 1: SPC simple point charge, recommended > 2: SPC/E extended simple point charge > 3: None > 1 > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b > Reading ../start.pdb... > Read 'TRYPSIN INHIBITOR', 604 atoms > Analyzing pdb file > Splitting chemical chains based on TER records or chain id changing. > There are 1 chains and 0 blocks of water and 58 residues with 604 atoms > > chain #res #atoms > 1 ' ' 58 604 > > All occupancies are one > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp > Atomtype 1 > Reading residue database... (gromos53a6) > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp > Using default: not generating all possible dihedrals > Using default: excluding 3 bonded neighbors > Using default: generating 1,4 H--H interactions > Using default: removing impropers on same bond as a proper > Residue 108 > Sorting it all out... > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb > Processing chain 1 (604 atoms, 58 residues) > Which LYSINE type do you want for residue 15 > 0. Not protonated (charge 0) (LYS) > 1. Protonated (charge +1) (LYSH) > > Type a number:1 > Which LYSINE type do you want for residue 26 > 0. Not protonated (charge 0) (LYS) > 1. Protonated (charge +1) (LYSH) > . > . skipping > . > Type a number:0 > Which GLUTAMIC ACID type do you want for residue 49 > 0. Not protonated (charge -1) (GLU) > 1. Protonated (charge 0) (GLUH) > > Type a number:0 > Identified residue ARG1 as a starting terminus. > Identified residue ALA58 as a ending terminus. > 8 out of 8 lines of specbond.dat converted successfully > Special Atom Distance matrix: > CYS5 CYS14 CYS30 CYS38 CYS51 MET52 > SG57 SG136 SG317 SG398 SG543 SD551 > CYS14 SG136 2.408 > CYS30 SG317 0.828 2.331 > CYS38 SG398 2.224 0.204 2.189 > CYS51 SG543 0.759 2.165 0.204 2.017 > MET52 SD551 0.928 2.703 0.373 2.560 0.550 > CYS55 SG585 0.204 2.316 0.664 2.137 0.573 0.805 > Link CYS-5 SG-57 and CYS-55 SG-585 (y/n) ?y > Link CYS-14 SG-136 and CYS-38 SG-398 (y/n) ?y > Link CYS-30 SG-317 and CYS-51 SG-543 (y/n) ?y > Select start terminus type for ARG-1 > 0: NH3+ > 1: NH2 > 2: None > 0 > Start terminus ARG-1: NH3+ > Select end terminus type for ALA-58 > 0: COO- > 1: COOH > 2: None > 0 > End terminus ALA-58: COO- > Checking for duplicate atoms.... > Now there are 58 residues with 604 atoms > Making bonds... > Number of bonds was 623, now 618 > Generating angles, dihedrals and pairs... > Before cleaning: 975 pairs > Before cleaning: 1187 dihedrals > Making cmap torsions...There are 329 dihedrals, 307 impropers, 906 angles > 975 pairs, 618 bonds and 0 virtual sites > Total mass 6517.563 a.m.u. > Total charge 6.000 e > Writing topology > > Writing coordinate file... > --------- PLEASE NOTE ------------ > You have successfully generated a topology from: ../start.pdb. > The Gromos53a6 force field and the spc water model are used. > --------- ETON ESAELP ------------ > > gcq#81: "Love is Like Moby Dick, Get Chewed and Get Spat Out" (Urban Dance > Squad) > > > Here are the relevant sections of the output topology file when using > GROMOS-53a6. > [ atoms ] > . > . skipping > . > ; residue 5 CYS rtp CYS2 q 0.0 > 53 N 5 CYS N 21 -0.31 14.0067 ; qtot > 0.69 > 54 H 5 CYS H 21 0.31 1.008 ; qtot 1 > 55 CH1 5 CYS CA 22 0 13.019 ; qtot 1 > 56 CH2 5 CYS CB 22 0 14.027 ; qtot 1 > 57 S 5 CYS SG 22 0 32.06 ; qtot 1 > 58 C 5 CYS C 23 0.45 12.011 ; qtot > 1.45 > 59 O 5 CYS O 23 -0.45 15.9994 ; qtot 1 > . > . skipping > . > ; residue 14 CYS rtp CYS2 q 0.0 > 132 N 14 CYS N 60 -0.31 14.0067 ; qtot > -0.31 > 133 H 14 CYS H 60 0.31 1.008 ; qtot 0 > 134 CH1 14 CYS CA 61 0 13.019 ; qtot 0 > 135 CH2 14 CYS CB 61 0 14.027 ; qtot 0 > 136 S 14 CYS SG 61 0 32.06 ; qtot 0 > 137 C 14 CYS C 62 0.45 12.011 ; qtot > 0.45 > 138 O 14 CYS O 62 -0.45 15.9994 ; qtot 0 > . > . skipping > . > ; residue 30 CYS rtp CYS2 q 0.0 > 313 N 30 CYS N 133 -0.31 14.0067 ; qtot > 3.69 > 314 H 30 CYS H 133 0.31 1.008 ; qtot 4 > 315 CH1 30 CYS CA 134 0 13.019 ; qtot 4 > 316 CH2 30 CYS CB 134 0 14.027 ; qtot 4 > 317 S 30 CYS SG 134 0 32.06 ; qtot 4 > 318 C 30 CYS C 135 0.45 12.011 ; qtot > 4.45 > 319 O 30 CYS O 135 -0.45 15.9994 ; qtot 4 > . > . skipping > . > ; residue 38 CYS rtp CYS2 q 0.0 > 394 N 38 CYS N 170 -0.31 14.0067 ; qtot > 3.69 > 395 H 38 CYS H 170 0.31 1.008 ; qtot 4 > 396 CH1 38 CYS CA 171 0 13.019 ; qtot 4 > 397 CH2 38 CYS CB 171 0 14.027 ; qtot 4 > 398 S 38 CYS SG 171 0 32.06 ; qtot 4 > 399 C 38 CYS C 172 0.45 12.011 ; qtot > 4.45 > 400 O 38 CYS O 172 -0.45 15.9994 ; qtot 4 > . > . skipping > . > ; residue 51 CYS rtp CYS2 q 0.0 > 539 N 51 CYS N 225 -0.31 14.0067 ; qtot > 5.69 > 540 H 51 CYS H 225 0.31 1.008 ; qtot 6 > 541 CH1 51 CYS CA 226 0 13.019 ; qtot 6 > 542 CH2 51 CYS CB 226 0 14.027 ; qtot 6 > 543 S 51 CYS SG 226 0 32.06 ; qtot 6 > 544 C 51 CYS C 227 0.45 12.011 ; qtot > 6.45 > 545 O 51 CYS O 227 -0.45 15.9994 ; qtot 6. > . > . skipping > . > ; residue 55 CYS rtp CYS2 q 0.0 > 581 N 55 CYS N 241 -0.31 14.0067 ; qtot > 6.69 > 582 H 55 CYS H 241 0.31 1.008 ; qtot 7 > 583 CH1 55 CYS CA 242 0 13.019 ; qtot 7 > 584 CH2 55 CYS CB 242 0 14.027 ; qtot 7 > 585 S 55 CYS SG 242 0 32.06 ; qtot 7 > 586 C 55 CYS C 243 0.45 12.011 ; qtot > 7.45 > 587 O 55 CYS O 243 -0.45 15.9994 ; qtot 7 > . > . skipping > . > [ bonds ] > . > . skipping > . > 56 57 2 gb_32 > 57 585 2 > 58 59 2 gb_5 > . > . skipping > . > 135 136 2 gb_32 > 136 398 2 > 137 138 2 gb_5 > . > . skipping > . > 316 317 2 gb_32 > 317 543 2 > 318 319 2 gb_5 > . > . skipping > . > [ angles ] > . > . skipping > . > 55 56 57 2 ga_16 > 56 57 585 2 > 55 58 59 2 ga_30 > . > . skipping > . > 134 135 136 2 ga_16 > 135 136 398 2 > 134 137 138 2 ga_30 > . > . skipping > . > 315 316 317 2 ga_16 > 316 317 543 2 > 315 318 319 2 ga_30 > . > . skipping > . > 396 397 398 2 ga_16 > 136 398 397 2 > 396 399 400 2 ga_30 > . > . skipping > . > 541 542 543 2 ga_16 > 317 543 542 2 > 541 544 545 2 ga_30 > . > . skipping > . > 583 584 585 2 ga_16 > 57 585 584 2 > 583 586 587 2 ga_30 > . > . skipping > . > [ dihedrals ] > . > . skipping > . > 53 55 58 60 1 gd_40 > 55 56 57 585 1 > 56 57 585 584 1 > 55 58 60 62 1 gd_14 > . > . skipping > . > 132 134 137 139 1 gd_40 > 134 135 136 398 1 > 135 136 398 397 1 > 134 137 139 141 1 gd_14 > . > . skipping > . > 313 315 318 320 1 gd_40 > 315 316 317 543 1 > 316 317 543 542 1 > 315 318 320 322 1 gd_14 > . > . skipping > . > 394 396 399 401 1 gd_40 > 396 397 398 136 1 > 396 399 401 403 1 gd_14 > . > . skipping > . > 539 541 544 546 1 gd_40 > 541 542 543 317 1 > 541 544 546 548 1 gd_14 > . > . skipping > . > 581 583 586 588 1 gd_40 > 583 584 585 57 1 > 583 586 588 590 1 gd_14 > . > . skipping > . > > > The GROMOS FFs all use a 'specbonds' section at the end of their ffbonded.itp > files, which looks like this (below is an excerpt from > gromos53a6.ff/ffbonded.itp): > > ; bond-, angle- and dihedraltypes for specbonds: > [ bondtypes ] > S S 2 gb_36 > NR FE 2 gb_34 > > [ angletypes ] > CH1 CH2 S 2 ga_16 > CH2 S S 2 ga_6 > CR1 NR FE 2 ga_34 > NR FE NR 2 ga_17 > > [ dihedraltypes ] > S S 1 gd_21 > NR FE 1 gd_38 > CH2 S 1 gd_26 > > while the other FFs do not use this method (as shown below). > > Elizabeths-MacBook-Pro:top elizabethploetz$ pwd > /usr/local/gromacs/share/gromacs/top > Elizabeths-MacBook-Pro:top elizabethploetz$ grep 'specbond' */* > gromos43a1.ff/ffbonded.itp:; bond-, angle- and dihedraltypes for specbonds: > gromos43a2.ff/ffbonded.itp:; bond-, angle- and dihedraltypes for specbonds: > gromos45a3.ff/ffbonded.itp:; bond-, angle- and dihedraltypes for specbonds: > gromos53a5.ff/ffbonded.itp:; bond-, angle- and dihedraltypes for specbonds: > gromos53a6.ff/ffbonded.itp:; bond-, angle- and dihedraltypes for specbonds: > > In a quick and dirty effort to mimic the other (working) FFs, I copied the > /usr/local/gromacs/share/gromacs/top/gromos53a6.ff files into my local > directory, commented out the 'specbonds' section of the ffbonded.itp file, > and re-ran pdb2gmx using the local files. This did not change the results > however. > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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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