Dear Modellers,
I am having a similar problem as Susan Crennell, whose mail you
answered on Nov, 3 . Unfortunately, your advice to correct the
alignment does not work in my case.
I am trying to model certain loops into an incomplete PDB-file
using other PDBs of related proteins as templates for the loops.
I used the following top-file:
INCLUDE
SET ALNFILE = 'WXY.ali'
SET KNOWNS = 'w' 'x' 'y'
SET SEQUENCE = 'target'
SET ATOM_FILES_DIRECTORY = './'
SET STARTING_MODEL= 1
SET ENDING_MODEL = 3
SET OUTPUT_CONTROL = 1 0 1 1
SET MD_LEVEL = 'refine1'
SET RSTRS_REFINED = 2
CALL ROUTINE = 'model'
with 3 templates (W, X, Y) and 1 target-sequence (each chain
contains ~650 AA), with Y as the incomplete PDB-file, X a different
PDB of the same (!) protein and W a related protein.
WXY.ali:
P1;w (structure related to Y and X)
structure:w:1::660:::::
WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW-WWWWWWWW---WWWWWWW--WWWWWWWWWW*
P1;x (same structure as Y, but different pdb-file)
structure:x:1::660:::::
------XXXXXXXXX---XXXXXXXXX-XXXX----XXXXXXXXXXX--XXXXXXXXX--XXXXXXXXXXXXXX*
P1;y (known structure)
structure:y:1::650:::::
------YYYYYYYYY-----YYYYYYYYYY-----YYYYYYYYYYYY--YYYYYYYYY--YYYYYYYYYYYYYY*
P1;target (sequence of known structure Y, including missing AA)
sequence:target::::::::
------TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT--TTTTTTTTT--TTTTTTTTTTTTTT*
I called up modeller (Version: mod_iris4d-IRIX5.3) under IRIX6.2 .
Approximately 15 min. after the initial model is written, Modeller4
cancels with an error in the log-file:
...
getrsr___> Numb of previous, current selected restraints: 56430 68752
mkspline_E> too many parameters, increase MPRMCNS
This error does _not_ occur when there are 5 templates, and 4 of them
are identical:
SET KNOWNS = 'w' 'y' 'y' 'y' 'y'
or 4 templates, and 3 of them are identical (etc...)
SET KNOWNS = 'w' 'y' 'y' 'y'
In these cases, I am getting an output with no errors at all, and with a
good-looking result, but as soon as I am trying to implement a third
template, the described error occurs.
What confuses me is the fact, that when I use just _two_ of these
together, there are no problems, no matter which templates I choose:
W and X : works (ini-file, restraints-file and schedule-file were
written out)
Y and X : works (same as above)
W and Y : works (same as above);
Using all three of them together seems to be impossible. I thought, if
there was a problem, then it was because of the slight structure change
between Y and X: maybe the difference was big enough to cause problems
with the structure of W - but modelling Y by using W and X was possible
- no errors !
In a normal log-file, after the selection of the restraints, the
SPLINE_RANGE is set; might a change in parameters help, or are there
simply to many restraints (using 1*W and 3*Y produces only 25000
restraints, not 68000) ?
I tried several other third templates, such as pdb-files that were
produced by Modeller4 in previous sessions and that are structurally
very close to Y, but then I get the error
addcc2_E> too many parameters, increase MPRMCNS .
I am grateful for any help you can offer me to solve this problem.
Thank you very much in advance,
Thorsten Schweikardt