VMD-L Mailing List

From: Eli Alster (ealster_at_caltech.edu)
Date: Tue Aug 13 2013 - 11:40:32 CDT

Hi,

I am experiencing an error when using the STAMP structural alignment
feature of Multiseq. I have two protein segments: a complete g-actin
protein and a fragment of the Arp2 protein. I want to align the
structurally homologous region of g-actin to the Arp2 fragment. If I put
the Arp2 fragment on top of the alignment list, and g-actin on the bottom
(so that the g-actin moves upon alignment), everything works. However, if I
reverse the order of the list because I would like the Arp2 fragment to
move to g-actin's location, the program fails with the error message "STAMP
alignment failed." This is followed by a 756 line error message.

Thanks,
Eli Alster
Caltech '14