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 - 13:00:02 PST
