[gmx-users] nucleic acid PDB input files

[Ken Rotondi]

Cameron,

As Andrey said, you are missing the information from your ff.hdb file. 
Easy to fix.

Go to whatever ff.itp file you are using and look up the hydrogens 
associated with the nucleotides in your structure. (you know that your 
forcefield includes these nucleotides since the warning is that a known 
residue, DGUA, is missing something)
I'll bet based upon the warning that you're using one of the gromos 
united atom forcefields, so only the three polar hydrogens need to be 
defined for DGUA.

Sketch the structure of DGUA on a piece of paper and name all the atoms 
using the names from the ff.itp file.

Identify the hydrogens that are named in the forcefield (i.e. H21, H22 
and H1) and go to section 5.5.2 of the gromacs manual. Using the naming 
rules there add entries into the appropriate ff.hdb file. For DGUA it 
would look like:

DGUA	2
		2	3	N2	C2	N1
		1	1	N1	C6	C4

When you read 5.5.2 this will make sense and you can do the same for 
the other nucleotides in your molecule.

Have fun,

Ken

PS. always ALWAYS check anything that a stranger gives you. I 
extrapolated the DGUA .hdb entry above from and RNA GUA .hdb entry I 
worked out. I'm (nearly) sure that the naming convention in the atoms 
in the bases would not change, but I don't know that. So checking that 
entry would be a great way to start.

K


On Feb 28, 2005, at 4:20 PM, 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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