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
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