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 ?
Thanks in advance !
Best regards!
Xiangqian Kong
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