Dear Pieter!
Initial alignment is porbably bad which is indicated in diagnostics of CHECK_ALIGNMENT and MALIGN3D. Please check your alignment manually or use FIT = on in MALIGN3D to produce correct alignment. If it won't help, then please send me .top, .pdb, alignment files and other necessary input files in separate attachments or as a tar.gz archive.
Happy landings,
Azat
Pieter Stouten wrote: > > 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/ > > ---------------------------------------------------------------------------- > > 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
-- - Dr. Azat Badretdinov - The Rockefeller Univ, Box 270 - 1230 York Ave, New York NY 10021, USA - Phone: (212) 327 7206 - Fax: (212) 327 7540 - E-mail: azat@salilab.org - WWW/URL: http://salilab.org/~azat