Dear all,
it seems that cpptraj crashes when trying to do a clustering analysis and requesting average structures for the clusters.
If I run the following script
trajin ../../../Trajectories/Production.mdcrd
cluster hieragglo epsilon 3.0 pairdist pairwisedistances.out savepairdist rms :70-74,336-340,369-374,394-402,429-434,453-458,478-482 mass summary cluster3.txt info cluster3info.txt repout cluster3rep
avgout cluster3avg
the output I get is
CPPTRAJ: Trajectory Analysis. V18.01 OpenMP
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 08/16/18 11:42:46
| Available memory: 21.034 GB
Reading '../../../Topology/AFB5_dry.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
INPUT: Reading input from 'cluster.in'
[trajin ../../../Trajectories/Production.mdcrd]
Reading '../../../Trajectories/Production.mdcrd' as Amber NetCDF
Warning: Trajectory box type is 'Trunc. Oct.' but topology box type is 'None'.
Warning: Setting topology box information from trajectory.
[cluster hieragglo epsilon 3.0 pairdist pairwisedistances.out savepairdist rms :70-74,336-340,369-374,394-402,429-434,453-458,478-482 mass summary cluster3.txt info cluster3info.txt repout
cluster3rep avgout cluster3avg]
CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:70-74,336-340,369-374,394-402,429-434,453-458,478-482]), mass-weighted best-fit
Hierarchical Agglomerative: epsilon 3.000, average-linkage.
Sieved frames will not be included in final cluster distance calculation.
Pairwise distance data set is 'pairwisedistances.out'
Saving pair-wise distances to 'pairwisedistances.out'
Cluster information will be written to cluster3info.txt
Summary of cluster results will be written to cluster3.txt
Representative frames will be chosen by lowest cumulative distance to all other frames.
Cluster representatives will be written to separate trajectories,
prefix (cluster3rep), format Amber Trajectory
Segmentation fault
Note that the analysis does not even start. In fact, it does not even start reading the trajectory.
Importantly, if I remove "avgout cluster3avg" from the script, the analysis completes without errors.
I am using Ambertools18, compiled with gcc 7.3.0. Also, please note that I did not experience this problem with Ambertools17, suggesting the possibility that this is a bug introduced in the latest
version.
Cheers,
Charo
--
Our new book on Synchronization phenomena is out: http://www.cambridge.org/9781107056268
Dr. Charo I. del Genio
University of Warwick
Gibbet Hill Road
Coventry CV4 7AL
UK
Tel: +44 (0)759 311 9487
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Received on Thu Aug 16 2018 - 04:00:02 PDT
