Dear all,

I’m working on a project in which we attempt to characterize the structural consequences of SNPs in HLA variants. I’ve used RoseTTAFold and AlphaFold to predict the 3D structures and generate PDB files that easily can be loaded into VMD (the newest version is 1.9.4 LATEST ALPHA (2022-04-27)). However, when I attempt to apply stamp structural alignment to compare with different HLA variants, it fails, showing the following at the end of the script (seemingly, the pairwise calculations are conducted correctly):

TREEWISE calculations

Reading in matrix file multiseq-6515605792643319.mat...

Doing cluster analysis...

Read: 2 Entries

CPU time: 0.000000 seconds

Setting up unclust

Setting up notparent

Setting up clust

CPU time: 0.000000 seconds

Single linkage on similarity

Doing Cluster Analysis...

child killed: unknown signal

while executing

"error $out"

(procedure "run" line 41)

invoked from within

"run "$tempDir" -f \"$filePrefix.scan\" -ATOMTYPE $atomTypeParam -prefix $filePrefix"

(procedure "::STAMP::alignStructures" line 78)

invoked from within

"::STAMP::alignStructures $regionSequenceIDs $scan $scanslide $scanscore $slowscan $npass"

I’ve tried with multiple different PDB files as well as re-installation of VMD, but nothing works. Only when I install version 1.9.3 (2016-11-30), the stamp structural alignment can run without any problems. Is anyone able to explain or come up with a solution that allows me to run the process in the newest version of VMD? Or does anyone know a similar program that I can utilize to obtain the same information?

Thanks so much in advance!