Hi,
It's important to check the errors and warnings printed by cpptraj. I
think the main issue is revealed by these messages:
Error: # atoms in current topology (19712) != # atoms in coords set
"muOR-trajectories" (19680)
Error: Setup failed for [createcrd]
Warning: Topology '02_6DDE_BU72_PAM_nowater.prmtop' selected # atoms
(19712) > original topology '01_6DDE_BU72_nowater.prmtop' (19680)
19712 atoms will be averaged for '02_6DDE_BU72_PAM_nowater.prmtop'.
These stem from the fact that you are reading in two trajectories that
correspond to different topologies (19680 vs 19712 atoms), but in many
of these commands you're not e.g. selecting a common subset of atoms.
If you want to perform a combined principal component analysis on both
trajectories, you should strip the trajectories down to a common
subset of atoms first. The procedure for doing this was recently
discussed on the mailing list; see
http://archive.ambermd.org/202106/0167.html
Also, if possible I recommend using a more updated version of cpptraj
(which should at least have better warnings and error checking). Hope
this helps,
-Dan
On Sat, Jul 10, 2021 at 6:53 PM Mac Kevin Braza <mebraza.up.edu.ph> wrote:
>
> I am running PCA script from the tutorial here
> https://amberhub.chpc.utah.edu/introduction-to-principal-component-analysis/
> by Galindo-Murillo, Roe, and Cheatham. I am confused on why the error after
> reading the concatenate trajectory says that
>
> "----- muOR-trajectories (1-100000, 1) -----
> PROJECTION: Calculating projection using eigenvectors 1 to 3 of myEvecs
> Start: 1 Stop: Final frame
> Atom Mask: [:972-1252&!.H*]
> Mask [:972-1252&!.H*] corresponds to 2256 atoms.
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Error: start 100001 > #Frames
> (100000), no frames will be processed.
> 1 errors encountered reading input.
> Error: Error(s) occurred during execution.
> 100% Complete."
>
> I included here my script and the output file. Is there anything that I
> am missing? Thank you in advance!
>
> Mac Kevin Braza
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Received on Tue Jul 13 2021 - 07:00:02 PDT
