Re: [AMBER] hydrogen bond charmm vs amber

From: Jason Swails <>
Date: Thu, 15 Jan 2015 14:32:51 -0500

On Thu, Jan 15, 2015 at 2:20 PM, newamber list <>

> 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

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jan 15 2015 - 12:00:02 PST
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