From: Aaron Oakley (
Date: Thu Sep 26 2019 - 20:40:31 CDT

Hello VMD-ers,

I am trying to run STAMP structure alignment within MultiSeq.

Every time I get the following.

STAMP Info) Running STAMP with command exec {/Applications/VMD} -f "multiseq-9701140075782845.start.domain" -scan 1 -scanslide 5 -scanscore 6 -slowscan 0 -n 2 -d "multiseq-9701140075782845.db.domain" -ATOMTYPE 0 -prefix multiseq-9701140075782845
MultiSeq Error)

STAMP Structural Alignment of Multiple Proteins
 by Robert B. Russell & Geoffrey J. Barton
 Please cite PROTEINS, v14, 309-323, 1992

It's a CA!!!
error: begin of sequence not found in PDB file
Error in domain 0 object 1
    while executing
"error $out"
    (procedure "run" line 41)
    invoked from within
"run "$tempDir" -f \"$filePrefix.start.domain\" -scan $scan -scanslide $scanslide -scanscore $scanscore -slowscan $slowscan -n $npass -d \"$filePrefix...."
    (procedure "::STAMP::alignStructures" line 75)
    invoked from within
"::STAMP::alignStructures $regionSequenceIDs $scan $scanslide $scanscore $slowscan $npass"

Help appreciated!