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

[David van der Spoel]

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?
>
> 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
>>>> -------------------------------------------------------
>>>>
>>>>
>>>
>>
>>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se