[gmx-users] nucleic acid PDB input files

[Maik Goette]

Hi

Concerning this error use -ignh as an option

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Cameron Mura wrote:
> Hi,
> Would anyone who's successfully used "pdb2gmx" to convert a DNA or RNA 
> starting structure in PDB format to Gromacs format please send me a 
> sample of their input PDB file?? I'd greatly appreciate it, as I can't 
> seem to get beyond errors of this sort when running pdb2gmx:
> 
>> ...
>> ...
>> Making bonds...
>>
>> WARNING: atom H21 is missing in residue DGUA 1 in the pdb file
>>          You might need to add atom H21 to the hydrogen database of 
>> residue DGUA
>>          in the file ff???.hdb (see the manual)
>>
>> WARNING: atom H22 is missing in residue DGUA 1 in the pdb file
>>          You might need to add atom H22 to the hydrogen database of 
>> residue DGUA
>>          in the file ff???.hdb (see the manual)
>>
>> WARNING: atom H1 is missing in residue DGUA 1 in the pdb file
>>          You might need to add atom H1 to the hydrogen database of 
>> residue DGUA
>>          in the file ff???.hdb (see the manual)
>>
>> Fatal error: There were 3 missing atoms in molecule Protein, if you 
>> want to use this incomplete topology anyhow, use the option -missing
> 
> 
> 
> Thanks,
> Cameron
> 
> 
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