Dear Justin and Mark, Thank you very much ! --- On Mon, 7/18/11, Mark Abraham <[email protected]> wrote:
> From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] PDB2GMX :There are 0 donors and 0 acceptors > To: "Discussion list for GROMACS users" <[email protected]> > 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 > -- gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search > before posting! > Please don't post (un)subscribe requests to the list. Use > the www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
