Hi all,
I am stumped with an issue I'm running into with cpptraj.
I have a trajectory that I've produced of a protein surrounded by ions. In
order to save disk space, I typically use ntwprt and print just the protein
atoms and the ions to the trajectory, and then set ntwr to a negative
number to save some snapshots along the way that contain all of the atoms.
I noticed recently that if I run the nativecontacts command to find
interactions between some protein atoms and the ions that the following
behavior occurs:
1. if I use the full parameter file (that has all atoms) and the final
ncrst file (that has all atoms) I get some larger number of contacts (let's
say 30 for example)
2. if I use the stripped parameter file (that has just the protein and ion
atoms) and load in the trajectory (which has the lower number of atoms due
to the use of ntwprt) and run the same nativecontacts command I get a very
different and much smaller number of ion interactions (looking also at the
last frame of that trajectory so it is comparable to the final ncrst file
that contains all atoms)
When using the cpptraj vector command on the trajectory (with smaller
number of atoms) and the ncrst file (that has all of the atoms), both
contain the box information (I do not strip with the nobox option included).
So why isn't cpptraj able to handle this if the box information is still
stored in the trajectory (and as far as I can tell, also in the parameter
files in the BOX DIMENSIONS section, both the full parameter and stripped
parameter file contain the same info there as well). Am I misunderstanding
something about how cpptraj handles a stripped parameter/trajectory file
pair?
Thanks for your help,
Joe
------
Joseph Baker, PhD
Barbara Meyers Pelson Chair in Faculty-Student Engagement (AY 2024-2027)
Professor, Department of Chemistry
The College of New Jersey
Ewing, NJ 08628
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Received on Thu Jul 09 2026 - 20:00:02 PDT
