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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Received on Thu Jan 15 2015 - 12:00:02 PST
