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

[David van der Spoel]

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.
>
> 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