Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology?

From: Daniel Roe <>
Date: Sat, 25 Sep 2021 15:10:21 -0400


Just a few points.

1) In addition to the manual, you can check what formats are supported
by the 'parm' and 'trajin' commands from the cpptraj interactive
prompt with 'help Formats trajin' and 'help Formats parm'.

2) To load coordinates in cpptraj (via 'trajin', 'loadcrd', etc), they
need to be associated with a topology (via 'parm') which describes
among other things how the atoms represented by the coordinates are
connected. In the PDB format, most of the connectivity is implied
instead of explicitly stated. So, for PDB files cpptraj attempts to
determine full connectivity by searching for bonds based on distance.
This works for the most part, but it's far better in general to use a
format that has explicit topology information (mol2, Amber parm,
charmm psf, etc).


On Sat, Sep 25, 2021 at 2:33 PM Matthew Guberman-Pfeffer
<> wrote:
> Thank you Thomas for the clarification, and Carlos, for the original replies.
> I misunderstand Carlos’s reply, and I apologize for that. I didn’t realize that one could do “parm <name>.pdb”.
> Best,
> Matthew
> > On Sep 25, 2021, at 2:23 PM, Thomas Cheatham <> wrote:
> >
> > *Message sent from a system outside of UConn.*
> >
> >
> > I'd say read the manual, but as Carlos said, load the PDB as a topology with the parm command. --tec3
> >
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Received on Sat Sep 25 2021 - 12:30:02 PDT
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