David van der Spoel wrote: > On 2010-08-16 14.44, Maiki wrote: >> David van der Spoel wrote: >>> On 2010-08-16 12.34, Maiki wrote: >>>> So, anybody knows why it does that or how to deal with nucleic acids? >>>> I only saw one similar question asked recently (with different error) >>>> which was also left without answer. >>> Not all force fields have complete support for DNA. Try Charmm. >> I tried all the forces I got with gromacs and they all failed with >> different errors (ok, amber worked, but I wanted to try gromos for some >> reasons). For charmm the error was: >> >> "There is a dangling bond at at least one of the terminal ends and >> the force field does not provide terminal entries or files. Edit a >> .n.tdb and/or .c.tdb file." > > did you run with the -ter option and select none? I did now, and it changed nothing for charmm. To be more precise it died before even asking me for dna termini. the last part of output is:
Opening force field file /home/maiki/share/gromacs/top/charmm27.ff/aminoacids.r2b Reading pfv-dna.pdb... Read 738 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 2 chains and 0 blocks of water and 17 residues with 738 atoms chain #res #atoms 1 'C' 19 392 2 'D' 17 346 All occupancies are one Opening force field file /home/maiki/share/gromacs/top/charmm27.ff/atomtypes.atp Atomtype 1 Reading residue database... (charmm27) Opening force field file /home/maiki/share/gromacs/top/charmm27.ff/aminoacids.rtp Residue 41 Sorting it all out... Opening force field file /home/maiki/share/gromacs/top/charmm27.ff/dna.rtp Residue 53 Sorting it all out... Opening force field file /home/maiki/share/gromacs/top/charmm27.ff/lipids.rtp Residue 65 Sorting it all out... Opening force field file /home/maiki/share/gromacs/top/charmm27.ff/rna.rtp Residue 77 Sorting it all out... Opening force field file /home/maiki/share/gromacs/top/charmm27.ff/aminoacids.hdb Opening force field file /home/maiki/share/gromacs/top/charmm27.ff/lipids.hdb Opening force field file /home/maiki/share/gromacs/top/charmm27.ff/aminoacids.n.tdb Opening force field file /home/maiki/share/gromacs/top/charmm27.ff/aminoacids.c.tdb Back Off! I just backed up pfv.top to ./#pfv.top.10# Processing chain 1 'C' (392 atoms, 19 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Identified residue DA1 as a starting terminus. Identified residue DA19 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully No suitable end (N or 5') terminus found in database - assuming this residue is already in a terminus-specific form and skipping terminus selection. No suitable end (C or 3') terminus found in database - assuming this residue is already in a terminus-specific form and skipping terminus selection. ------------------------------------------------------- Program pdb2gmx_d, VERSION 4.5-beta2 Source code file: pdb2top.c, line: 883 Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I removed chain A(protein) and hetatms, only left C and D of double DNA helix. >> >> so, it looks that charmm also tries to find N- and C- termini (or I >> don't understand the error message which is also more than possible) >> Besides, gromos does recognise DNA base pairs (DTHY for thymine etc, >> they are in ff files) and all its atoms, only in the end it asks this >> stupid question 'where is my NH3+ group?' and fails... >> >> There may be something with my pdb format but that's what I got from >> rcsb/pdb. Is there a canonical description of PDB format expected by ffs >> in pdb2gmx so I could correct my input myself? (if it's going to help) >> >>>> >>>> Maiki wrote: >>>>> Hi, >>>>> >>>>> I'm trying to convert protein-DNA complex using pdb2gmx with >>>>> gromos53a6.ff >>>>> >>>>> $ pdb2gmx -f del.pdb -o del.gro -p del.top -i del.itp -n del.ndx >>>>> -ignh >>>>> >>>>> In gromacs version 4.5-beta2 the result is: >>>>> >>>>> Processing chain 3 'C' (516 atoms, 25 residues) >>>>> There are 0 donors and 0 acceptors >>>>> There are 0 hydrogen bonds >>>>> Identified residue DT1 as a starting terminus. >>>>> Identified residue DA25 as a ending terminus. >>>>> 8 out of 8 lines of specbond.dat converted successfully >>>>> Warning: 'DT' not found in residue topology database, trying to use >>>>> 'DTHY' >>>>> Start terminus: NH3+ >>>>> Warning: 'DA' not found in residue topology database, trying to use >>>>> 'DADE' >>>>> End terminus: COO- >>>>> Warning: 'DT' not found in residue topology database, trying to use >>>>> 'DTHY' >>>>> Warning: 'DA' not found in residue topology database, trying to use >>>>> 'DADE' >>>>> Warning: 'DG' not found in residue topology database, trying to use >>>>> 'DGUA' >>>>> (...) >>>>> Warning: 'DA' not found in residue topology database, trying to use >>>>> 'DADE' >>>>> >>>>> ------------------------------------------------------- >>>>> Program pdb2gmx, VERSION 4.5-beta2 >>>>> Source code file: pdb2top.c, line: 922 >>>>> >>>>> Fatal error: >>>>> atom N not found in buiding block 1DT while combining tdb and rtp >>>>> For more information and tips for troubleshooting, please check the >>>>> GROMACS >>>>> website at http://www.gromacs.org/Documentation/Errors >>>>> ------------------------------------------------------- >>>>> >>>>> >>>> >>> >>> >> > >
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