From: Vermaas, Joshua (
Date: Fri Sep 27 2019 - 13:23:03 CDT

The error appears to be related to Stamp not recognizing the protein within the loaded structure. Is there anything squirrelly about your pdb? I've used it before from solvated protein pdbs built in VMD itself, but depending on your system preparation and what is available to VMD from what you've loaded, Stamp may not have what it needs to be successful, and that is what you are seeing. Attaching your structure files probably will be required to sort out what is going on.


On 2019-09-26 20:45:20-06:00 wrote:

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!