We have a problem building a 2-domain protein based on multiple (8) other proteins. We put a slash between the two domains so that Modeller knows not to connect the termini. We have no problems with large distances between equivalent CA's of different proteins. the only unusual aspect we notice is that the pair of warnings (?) "drmsq1__W> n<2 and drmsq3__W> n<2" occurs 19 times. No error message occurs, but no model is produced either. Please find attached part of the output. Hope this is enough for the experts on ths list to give us hints as to how to resolve this issue.
Thanks a million,
Pieter Stouten pieter.stouten@dupontmerck.com DuPont Merck - Computer Aided Drug Design Group Web: http://www.halcyon.com/stouten/
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chkaln___> Checking pairwise structural superpositions: Equivalent CA pairs with distance difference larger than 6.0 angstroms:
ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- drmsq1__W> n<2 drmsq3__W> n<2
[... repeated 19 times ... /PFWS]
chkaln___> Checking structure-sequence alignments: Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ----------------------------------------------
<< end of CHECK_ALIGNMENT.
TOP______> 109 94 CALL ROUTINE = BUILD_METHOD
TOP______> 110 66 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS
[...]
TOP______> 111 67 MALIGN3D FIT = OFF, GAP_PENALTIES_3D = 0 4
malign3d_> Initial framework positions: 9 fit2xyz_E> number of equivalent positions < 3: 0 recover__> MODELLER_STATUS >= CONTROL: 1 1