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

[ÏéÇ« ¿×]

Dear Justin and Mark,
  Thank you very much !

--- On Mon, 7/18/11, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] PDB2GMX :There are 0 donors and 0 acceptors
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Monday, July 18, 2011, 6:16 AM
> 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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