I edited the grompp output and sent it to you. Bring that again here: Generated 21528 of the 21528 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 18355 of the 21528 1-4 parameter combinations
ERROR 1 [file topol.top, line 414]: No default Bond types ERROR 2 [file topol.top, line 1698]: No default U-B types ERROR 3 [file topol.top, line 1699]: No default U-B types ERROR 4 [file topol.top, line 2345]: No default Proper Dih. types ERROR 5 [file topol.top, line 2346]: No default Proper Dih. types ERROR 6 [file topol.top, line 3278]: No default Improper Dih. types And wrote line 414 is : line 414 of topol.tp: [bonds] 1 2 1 Sincerely, Shima ________________________________ From: Mark Abraham <mark.abra...@anu.edu.au> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Tuesday, July 31, 2012 4:40 AM Subject: Re: [gmx-users] Diagnosing + system blowing up On 31/07/2012 7:16 AM, Shima Arasteh wrote: > Wow! That was a fabulous explanation given to me. Thanks dear Mark! :-) > > I regenerated the topol.top to check the correctness of input and FF files. > Some output has been changed however a little bit. Now, I bring you all was > needed again: > >> 1. rtp entry >> >> [ FVAL ] > [ atoms ] > CN C 0.357 0 > ON O -0.51 1 > H1 HA 0.100 2 > N NH1 -0.423 3 > HN H 0.333 4 > CA CT1 0.034 5 > HA HB 0.09 6 > CB CT1 -0.093 7 > HB HA 0.09 8 > CG1 CT3 -0.268 9 > HG11 HA 0.09 10 > HG12 HA 0.09 11 > HG13 HA 0.09 12 > CG2 CT3 -0.268 13 > HG21 HA 0.09 14 > HG22 HA 0.09 15 > HG23 HA 0.09 16 > C C 0.528 17 > O O -0.510 18 > [ bonds ] > CN H1 > CN ON > CN N > N HN > CA N > CA HA > CA C > C O > CA CB > CB HB > CB CG1 > CB CG2 > CG2 HG21 > CG2 HG22 > CG2 HG23 > CG1 HG11 > CG1 HG12 > CG1 HG13 > > [ impropers ] > CN N ON H1 > >> 2. hdb entry > In which file? > *aminoacids.hdb > > >> FVAL 6 >> 1 1 H1 CN N ON > This should be generating H1 bonded to CN... > >> 1 1 HN N C CA >> 1 5 HA CA N C CB >> 1 5 HB CB CA CG1 CG2 >> 3 4 HG1 CG1 CB CA >> 3 4 HG2 CG2 CB CA >> >> 3. N-terminal fragment >> HETATM 1 CN FVAL 1 -0.721 1.600 1.249 >> HETATM 2 ON FVAL 1 -0.839 2.806 1.453 >> ATOM 3 N FVAL 1 -1.227 0.728 2.125 >> ATOM 4 CA FVAL 1 -1.918 1.159 3.323 >> ATOM 5 C FVAL 1 -1.969 2.678 3.410 >> ATOM 6 O FVAL 1 -0.931 3.335 3.447 >> ATOM 7 CB FVAL 1 -1.219 0.644 4.576 >> ATOM 8 CG1 FVAL 1 0.208 1.178 4.618 >> ATOM 9 CG2 FVAL 1 -1.976 1.118 5.812 >> >> 4. pdb2gmx command >> #pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter >> >> 5. pdb2gmx output > Using the Charmm36-modified force field in directory ./charmm36-modified.ff > > Opening force field file ./charmm36-modified.ff/aminoacids.r2b > Opening force field file ./charmm36-modified.ff/rna.r2b > Reading monomer.pdb... > Read 177 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 24 residues with 177 atoms > > chain #res #atoms > 1 ' ' 24 177 > > All occupancy fields zero. This is probably not an X-Ray structure > Opening force field file ./charmm36-modified.ff/atomtypes.atp > Atomtype 1 > Reading residue database... (charmm36-modified) > Opening force field file ./charmm36-modified.ff/aminoacids.rtp > Residue 42 > Sorting it all out... > Opening force field file ./charmm36-modified.ff/dna.rtp > Residue 46 > Sorting it all out... > Opening force field file ./charmm36-modified.ff/lipids.rtp > Residue 82 > Sorting it all out... > Opening force field file ./charmm36-modified.ff/rna.rtp > Residue 86 > Sorting it all out... > Opening force field file ./charmm36-modified.ff/aminoacids.hdb > Opening force field file ./charmm36-modified.ff/dna.hdb > Opening force field file ./charmm36-modified.ff/lipids.hdb > Opening force field file ./charmm36-modified.ff/rna.hdb > Opening force field file ./charmm36-modified.ff/aminoacids.n.tdb > Opening force field file ./charmm36-modified.ff/dna.n.tdb > Opening force field file ./charmm36-modified.ff/rna.n.tdb > Opening force field file ./charmm36-modified.ff/aminoacids.c.tdb > Opening force field file ./charmm36-modified.ff/dna.c.tdb > Opening force field file ./charmm36-modified.ff/rna.c.tdb > > Back Off! I just backed up topol.top to ./#topol.top.2# > Processing chain 1 (177 atoms, 24 residues) > Identified residue FVAL1 as a starting terminus. > Identified residue GLY24 as a ending terminus. > 8 out of 8 lines of specbond.dat converted successfully > Select start terminus type for FVAL-1 > 0: NH3+ > 1: NH2 > 2: None > 2 > Start terminus FVAL-1: None > Select end terminus type for GLY-24 > 0: COO- > 1: COOH > 2: CT2 > 3: CT3 > 4: None > 0 > End terminus GLY-24: COO- > Opening force field file ./charmm36-modified.ff/aminoacids.arn > Opening force field file ./charmm36-modified.ff/dna.arn > Opening force field file ./charmm36-modified.ff/rna.arn > Checking for duplicate atoms.... > Now there are 24 residues with 360 atoms > Making bonds... > Number of bonds was 362, now 362 > Generating angles, dihedrals and pairs... > Before cleaning: 925 pairs > Before cleaning: 930 dihedrals > Keeping all generated dihedrals > Making cmap torsions...There are 22 cmap torsion pairs > There are 930 dihedrals, 49 impropers, 644 angles > 916 pairs, 362 bonds and 0 virtual sites > Total mass 2510.906 a.m.u. > Total charge 1.000 e > Writing topology > > Back Off! I just backed up posre.itp to ./#posre.itp.1# > > Writing coordinate file... > > Back Off! I just backed up monomer.gro to ./#monomer.gro.1# > --------- PLEASE NOTE ------------ > You have successfully generated a topology from: monomer.pdb. > The Charmm36-modified force field and the tip3p water model are used. > --------- ETON ESAELP ------------ > > >> 6. N-terminal fragment of the grompp -c input > 1FVAL CN 1 3.039 1.904 2.416 > 1FVAL H1 2 3.086 1.871 2.334 This H1 atom is now in the right position for generation from the correct .hdb, and pdb2gmx is not complaining of the long bond to H1, which I think means you are using the correct .hdb now, and were not doing so earlier. So my suggestion of a bug was unfounded. > 1FVAL ON 3 3.027 2.025 2.436 > 1FVAL N 4 2.988 1.817 2.504 > 1FVAL HN 5 3.029 1.759 2.433 > 1FVAL CA 6 2.919 1.860 2.623 > 1FVAL HA 7 2.828 1.821 2.614 > 1FVAL CB 8 2.989 1.808 2.749 > 1FVAL HB 9 2.991 1.708 2.747 > 1FVAL CG1 10 3.132 1.862 2.753 > 1FVAL HG11 11 3.178 1.828 2.835 > 1FVAL HG12 12 3.181 1.831 2.672 > 1FVAL HG13 13 3.130 1.962 2.754 > 1FVAL CG2 14 2.913 1.856 2.872 > 1FVAL HG21 15 2.959 1.822 2.954 > 1FVAL HG22 16 2.911 1.956 2.874 > 1FVAL HG23 17 2.820 1.821 2.869 > 1FVAL C 18 2.914 2.012 2.632 > 1FVAL O 19 3.018 2.077 2.636 > > ... and this shows atom H1 around 0.1nm from atom C. I can think of no > legitimate reason how this could occur, given your stated .hdb, but I > seem to recall an old .hdb version you showed had a line > > 1 1 H1 C N ON > > rather than the correct > > 1 1 H1 CN N ON > > ********* I checked it, there was the correct one. > > and this would explain the weird H1 position perfectly (but not how it still > gets bonded to atom 1). I'd like you to double check that > ./charmm36-modified.ff/aminoacids.hdb has (only) the correct FVAL entry. > Also, I'd like to see the first 30 or so lines of the [bonds] section of this > [moleculetype] in topol.top, so we can really see what bonds are generated. > > * First 50 lines of the [bonds] section: These are now normal. I suspect they were not earlier. > > [ bonds ] > ; ai aj funct c0 c1 c2 c3 > 1 2 1 > 1 3 1 > 1 4 1 > 4 5 1 > 4 6 1 > 6 7 1 > 6 8 1 > 6 18 1 > 8 9 1 > 8 10 1 > 8 14 1 > 10 11 1 > 10 12 1 > 10 13 1 > 14 15 1 > 14 16 1 > 14 17 1 > 18 19 1 > 20 21 1 > 20 22 1 > 22 23 1 > 22 24 1 > 22 29 1 > 24 25 1 > 24 26 1 > 24 27 1 > 27 28 1 > 29 30 1 > 29 31 1 > 31 32 1 > 31 33 1 > 33 34 1 > 33 35 1 > 33 48 1 > 35 36 1 > 35 37 1 > 35 38 1 > 38 39 1 > 38 40 1 > 38 44 1 > 40 41 1 > 40 42 1 > 40 43 1 > 44 45 1 > 44 46 1 > 44 47 1 > 48 49 1 > 48 50 1 > 50 51 1 > 50 52 1 > > > I think you may have encountered a new bug in pdb2gmx. > >> 1FVAL O 19 3.019 2.076 2.635 >> >> 7.grompp command line >> # grompp -f ions.mdp -c monomer_solv.gro -p topol.top -o ions.tpr >> >> >> 8. grompp output >> Generated 21528 of the 21528 non-bonded parameter combinations >> Generating 1-4 interactions: fudge = 1 >> Generated 18355 of the 21528 1-4 parameter combinations >> >> ERROR 1 [file topol.top, line 414]: >> No default Bond types >> >> >> ERROR 2 [file topol.top, line 1698]: >> No default U-B types >> >> >> ERROR 3 [file topol.top, line 1699]: >> No default U-B types >> >> >> ERROR 4 [file topol.top, line 2345]: >> No default Proper Dih. types >> >> >> ERROR 5 [file topol.top, line 2346]: >> No default Proper Dih. types >> >> ERROR 6 [file topol.top, line 3278]: >> No default Improper Dih. types > All this probably follows on from the confused state of bonding to H1, > e.g. if CN-H1 is defined from the .rtp bond, and there's now a C-H1 from > the possibly erroneous .hdb construction. What is line 414 of topol.top? > > * line 414 of topol.tp: > [bonds] > 1 2 1 That's what it is in the new version, not the old version that actually had the errors. What does grompp have to say now? Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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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