Hi,
On Thu, Jan 15, 2015 at 2:00 PM, newamber list <newamberlist.gmail.com> wrote:
> 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.
Right. This is why 'nastruct' has only a distance cutoff keyword for
hydrogen bonds ('hbcut') and not one for angles.
-Dan
>
>
> 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
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> 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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--
-------------------------
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 - 13:30:03 PST
