Hi Fred,
From memory, this can occur due to long bond lengths in the model being
interpreted as chain breaks, try editing the generate.inp or
generate_easy.inp script and increase the value for "break_cutoff":
{* cutoff distance in Angstroms for identification of breaks *}
{* the default of 2.5A should be reasonable for most cases. If the input
structure has bad geometry it may be necessary to increase this
distance *}
{===>} break_cutoff=2.5;
You may also try switching off the automatic detection of mainchain breaks:
* automatically detect mainchain breaks in proteins based on distance *}
{* the peptide link at break points will be removed *}
{+ choice: true false +}
{===>} auto_break=true;
It is also worth checking that the offending residues have their full
complement of backbone atoms in appropriate places (not accidentally
zapped to far-flung regions of coordinate space).
Cheers,
James
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