I am running the ddg_monomer with the high-resolution protocol. I am getting this error:
ERROR: seqpos >= 1
What does this usually mean?
Normally when you see error messages that have that sort of mathematical statement in them, they're comming from "assertions" in the code. That is, there's a place in the code which is asserting that "seqpos >= 1". It's when this test fails that it prints the error message. So the error message is being printed because seqpos is equal to zero.
A (pose numbered) sequence position of zero is used in many places in the code to represent a default, invalid value. Or in other words, there's some place where a sequence position should be set, but isn't.
It's somewhat hard to say without more context which particular setting is not being set appropriately. Sometimes you can tell by looking at the surrounding messages which have been printed, as to what Rosetta was doing at the time that it encountered an unset sequence position. The other possibility is to look through your flags and input files, looking for things which might be missing or mis-specified.