AMBER Archive (2004)

Subject: AMBER: using ptraj

From: Carsten Detering (
Date: Tue Jul 27 2004 - 16:10:02 CDT

Dear ambers,

I have some trouble with a set of my trajectory files (complex, receptor
and ligand), which I would like to prepare for mm_pbsa.
this is my command sequence:

ptraj my_parmfile_with_water_and_ions.prm
trajin my_trajectory_file_from_sander.mdcrd
trajout test.crd
center :first_residue_in_complex-last_residue_in_complex
strip :WAT
strip :Na+

When I then run, the calculation crashes, and the
sander.1.out file contains the error message:

FATAL: NATOM mismatch in coord and topology files

I checked the output from ptraj concerning the number of atoms (when the
program masks the atoms for imaging), and the NATOMS is the same as in
the parameter files which dont contain waters and counter ions.
Looking at the frames in vmd, it seems like all the water molecules (or
at least a part of them) are concentrated in the protein now, and their
atoms overlaying with the atoms of the protein.

Could someone please point out to me what is wrong here?

Thanks in advance,


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