[gmx-users] pdb2gmx-4.5 treats DNA as protein (and fails)

[Maiki]

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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