Hi Jason,
Thanks.
>> Cpptraj recognizes the names used by the Amber residue templates where
that information is relevant
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.
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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Received on Thu Jan 15 2015 - 12:30:03 PST
