Re: [AMBER] Backbone

From: Jason Swails <>
Date: Wed, 18 Nov 2015 09:12:57 -0500

On Wed, Nov 18, 2015 at 8:15 AM, mohammad r <>

> Hi Karl,
> No I received it from my supervisor and I don't know what it means.

​I suspect your advisor said/meant "the backbone is a mess", meaning that
the secondary and tertiary structures are either nonsensical or not
expected. But that's just a guess. You should be asking your advisor what
they meant, not us.

> Is cpptraj analysis tool a good software for checking all bonds, angles
> and dihedrals.

​Sure. But there is no "check all bonds/angles/dihedrals". There is the
"check" command that looks for overlaps and long bonds. There is also the
distance, angle, dihedral, and multidihedral commands that will measure
specific bonds, angles, and dihedrals, but you have to supply the
distances/angles/dihedrals you want to be calculated.

Excuse me, do you know any source for building pdb file from protein
> structure?

​I don't know what you mean by "protein structure". The protein structure
is always defined in some kind of file. Many times it's a PDB file. Other
file formats also exist -- mol2, PDBx/mmCIF, Amber prmtop/inpcrd, CHARMM
PSF/crd, Gromacs GRO, .... If you do not have a PDB file, you can create
one using a program that converts between file formats. cpptraj does this,
as does openbabel.

In general, you need to be MUCH more specific with your questions on this
list if you want better help.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Nov 18 2015 - 06:30:05 PST
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