[gmx-users] PDB2GMX :There are 0 donors and 0 acceptors

[Mark Abraham]

On 18/07/2011 1:41 AM, Justin A. Lemkul wrote:
>
>
> ÏéÇ« ¿× wrote:
>> Dear Gromacs Users,
>>   When I use the pdb2gmx command on my protein-DNA complex, for the A 
>> chain which consists of the protein.pdb2gmx told me as follows:
>> Processing chain 1 'A' (1222 atoms, 151 residues)
>> There are 243 donors and 215 acceptors
>> There are 285 hydrogen bonds
>> Will use HISE for residue 262
>> Identified residue ACE139 as a starting terminus.
>> Identified residue NME289 as a ending terminus.
>> 8 out of 8 lines of specbond.dat converted successfully
>> Special Atom Distance matrix:
>>    However, for the C and D chain which consists of the DNA, it told 
>> me that like follows:
>> Processing chain 2 'C' (365 atoms, 15 residues)
>> There are 0 donors and 0 acceptors
>> There are 0 hydrogen bonds
>> Identified residue DC1 as a starting terminus.
>> Identified residue DT15 as a ending terminus.
>> 8 out of 8 lines of specbond.dat converted successfully
>>
>>    My puzzle is about the number of donors and acceptors that pdb2gmx 
>> told me.For protein, it seems ok,but for DNA, there none donors or 
>> acceptors. However, there are many oxygen or nitrogen atoms on DNA, i 
>> think they should be regarded as donors or acceptors.
>>    Therefore, why does pdb2gmx reported like that?  Does it influence 
>> the following simulations or trajectory analysis, such as g_hond and 
>> so on ?
>
> For pdb2gmx, donors and acceptors are only relevant for determining 
> the protonation state of histidine residues.  For DNA, there are no 
> HIS, so the output will always show zero.  There is nothing wrong.

I've fixed pdb2gmx to only show this output when relevant, and to be a 
little less cryptic about what is going on :-)

Mark