AMBER Archive (2008)

Subject: Re: AMBER: loadPdb returns extra atoms

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Mon Apr 14 2008 - 14:19:03 CDT

> I am simply trying to use ptraj to create an average pdb structure. My
> file has 574 atoms. When I load it into leap it says "574 atoms." I save
> the .prmtop and then use it with ptraj to run my ptraj script. The
> message I get is:
>
> WARNING in ptrajProcessInputCoordinates(): Unexpected number of atoms
> encountered when reading PDB!
> loadPdb returned 579
> getCoordinatesFromPdb returned 574
> actual number of atoms is 574
>
> How is this possible? Where are these atoms comming from and what can I do
> to solve this? Thank you for any help or advice.

I think all is OK; I need to update the output from ptraj here. As far as
coordinates go, 574 atoms were found which matches your PDB so all is OK.
The extra are probably other lines in the PDB file (such as REMARK, TER,
etc). That error/warning message should not be printed when the number of
coordinates matches the number of atoms i.e. when 574=574 (i.e. I was
probably checking the loadPdb return value to the number of atoms
incorrectly/inaccurately).

-- tec3
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