Hi,
Can you provide the version of cpptraj you are using along with the
exact input(s) (and outputs if you have them handy)?
Also, if you get a chance please send me off-list some files I can use
to reproduce the behavior you see. Thanks,
-Dan
On Thu, Jul 9, 2026 at 10:46 PM Baker, Joseph via AMBER
<amber.ambermd.org> wrote:
>
> 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 Fri Jul 10 2026 - 05:00:02 PDT
