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Problem building 2-domain protein



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 <>
DuPont Merck - Computer Aided Drug Design Group
Web: http://www.halcyon.com/stouten/

----------------------------------------------------------------------------

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