Hi Daniel,
Thanks for clarification. I was not expecting that nacstruct does not
consider 'Hydrogens' for H-bonds. I gave a quick look in paper reference
you provided. What I guess is, if one wants to define a H-bond using
crystal structure definition as standard reference then we can use only
heavy atoms (resolution issues) so 3DNA/nastruct considers only heavy atoms.
thanks,
Jiom
On Thu, Jan 15, 2015 at 8:42 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Thu, Jan 15, 2015 at 1:06 PM, newamber list <newamberlist.gmail.com>
> wrote:
> > I just checked hydrogens considered while calculating H-bonds between
> base
> > pairs have same name in CHARMM and AMBER and that is why CPPTRAJ does not
> > complain (not relevant or not required information). Only few H names are
> > different which I think are never involved in any other DNA geometry
> > calculations (like twist, shear etc.) and thus cpptraj does not complain
> > about them.
>
> Actually the 'nastruct' command doesn't care about hydrogen atoms. The
> nucleic acid reference frames are only defined by heavy atoms. As
> Jason mentioned, the Amber atom names by and large correspond to the
> ones used in PDBs. FYI, the reference frame definitions used are the
> same ones used by 3DNA, defined in this publication:
>
> http://www.sciencedirect.com/science/article/pii/S0022283601949873
>
> If you are interested they are defined in
> $AMBERHOME/AmberTools/src/cpptraj/src/AxisType.cpp, right at the top.
>
> -Dan
>
> >
> > regards,
> > JIom
> >
> >
> >
> > On Thu, Jan 15, 2015 at 7:32 PM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> >> On Thu, Jan 15, 2015 at 2:20 PM, newamber list <newamberlist.gmail.com>
> >> wrote:
> >>
> >> > Hi All,
> >> >
> >> > I have one DNA pdb with AMBER (ff10) atom names and same file with
> >> CHARMM36
> >> > atom names. Mainly difference are AMBER's C7, OP1, OP2 with their
> >> > respective names in CHARMM36 being C5M, O1P, O2P. Also there are many
> H
> >> > names differences.
> >> >
> >> > I used these DNA pdbs to calculate number of Hydrogen bonds with
> cpptraj
> >> > natstruc but cpptraj complained about C5M atom in CHARMM case. After
> >> > correcting heavy atom names I got no error and found same number of H
> >> > bonds.
> >> >
> >> > I am getting correct results but just wondering as cpptraj does not
> >> > complain about expected H name (AMBER) as they are different in AMBER
> and
> >> > CHARMM. Is it due to somehow programme searches for generic *H* kind
> >> name?
> >> >
> >>
> >> Cpptraj recognizes the names used by the Amber residue templates where
> >> that information is relevant -- it is written, after all, by an Amber
> >> developer. :)
> >>
> >> But Amber names its hydrogens according to the PDB standard (that is,
> the
> >> hydrogen atom names in the Amber topology
> >>
> >> file is the same as what the PDB standard mandates for PDB files at
> >> RCSB). So I would say that, in this case, CHARMM Is the odd man out
> here.
> >> I have no idea why they would do this, but presumably there is (was?) a
> >> reason?
> >>
> >> Good luck,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> BioMaPS,
> >> Rutgers University
> >> Postdoctoral Researcher
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Thu Jan 15 2015 - 13:30:02 PST
