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

[Justin A. Lemkul]

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.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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