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

[Maiki]

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."

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
>>> -------------------------------------------------------
>>>
>>>
>>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100816/a543d678/attachment.html>