AMBER Archive (2008)

Subject: AMBER: loadPdb returns extra atoms

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Mon Apr 14 2008 - 13:50:32 CDT

Dear AMBER users,

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.

Thanks,
Seth

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