Dear modeller, I was using still modeller 4 (just to complete one work that I was doing) I have one problem, I m building a model using 7 templates (I made a structural alignment that I am using to build my model). Everything works fine... except that for one situation (so my input file top and ali are correspondent, except the sequence that I have to model... like you can immagine)
and I have this message:
mkspline_E> too many parameters, increase MPRMCNS
if I remove one template it works fine...
what does it mean this message? how can I still use 7 templates?
Luca
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Luca Settimo Molecular Structures and Biocomputing Department of Biochemistry and Pharmacy Åbo Akademi University Tykistökatu 6A 20520 Turku Finland phone: +358 (0) 2 2154600 fax: +358 (0) 2 2153280 mobile phone: +358 50 5238418 mailto:lsettimo@abo.fi http://www.abo.fi/~lsettimo
The alignment probably aligns residues in known structures that are quite far in space, requiring a lot of memory for the splines to describe the corresponding multi-modal gaussian functions (this is probably the same problem that was discussed here last week or so). The solution is to improve the alignment (by only aligning residues that can be aligned close in space; close meaning about 5A or better; and not aligning residues that are further apart); possibly, MODELLER6v1 is a little less stingy with memory assignment for splines, so maybe it would work on your current alignment.
Best wishes, Andrej
-- Andrej Sali, Associate Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali@rockefeller.edu; http://salilab.org
-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of Luca Settimo Sent: Monday, February 18, 2002 9:45 AM To: 'Modeller Usage List' Subject: mkspline_E
Dear modeller, I was using still modeller 4 (just to complete one work that I was doing) I have one problem, I m building a model using 7 templates (I made a structural alignment that I am using to build my model). Everything works fine... except that for one situation (so my input file top and ali are correspondent, except the sequence that I have to model... like you can immagine)
and I have this message:
mkspline_E> too many parameters, increase MPRMCNS
if I remove one template it works fine...
what does it mean this message? how can I still use 7 templates?
Luca
...................................................................
Luca Settimo Molecular Structures and Biocomputing Department of Biochemistry and Pharmacy Åbo Akademi University Tykistökatu 6A 20520 Turku Finland phone: +358 (0) 2 2154600 fax: +358 (0) 2 2153280 mobile phone: +358 50 5238418 mailto:lsettimo@abo.fi http://www.abo.fi/~lsettimo
hello Luca,
You need to be sure that the templates superpose reasonable well and can be aligned to the target, (reasonable well). I think this error comes up, if the produced alignment is 50% or twice longer as the input sequences, i.e. no reasonable starting framework can be produced.
There is a slight chance that modeller fools you (depending on which older version you use): try to put the longest template sequence as the first in the alignment in the ali file and call it first from the top file when defining templates.
If it does not work, take a look at the superposed structures and remove the one which is the most divergent from the rest.
If case you use fully automated modeller, than another step would be to produce the input alignment among the templates and target separately, and provide it as an input to modeller (and be sure that the length of the alignment is not unreasonable longer than the input sequences).
in fact, there is a chance that in older versions problems with spline restraints can be produced with extremely similar input templates too ...
I think it is a good idea that you stick with mod4 to finish your project, however you can get more help in the future if you switch to the newest version, that is currently mod6v1, downloadable from our web site. We are not going to fix any problems in these 5-6 year old codes.
best wishes, Andras
Luca Settimo wrote: > > Dear modeller, > I was using still modeller 4 (just to complete one work that I was > doing) > I have one problem, I m building a model using 7 templates (I made a > structural alignment that I am using to build my model). > Everything works fine... > except that for one situation (so my input file top and ali are > correspondent, except the sequence that I have to model... like you can > immagine) > > and I have this message: > > mkspline_E> too many parameters, increase MPRMCNS > > if I remove one template it works fine... > > what does it mean this message? how can I still use 7 templates? > > Luca > > ................................................................... > > Luca Settimo > Molecular Structures and Biocomputing > Department of Biochemistry and Pharmacy > Åbo Akademi University Tykistökatu 6A 20520 Turku Finland > phone: +358 (0) 2 2154600 > fax: +358 (0) 2 2153280 > mobile phone: +358 50 5238418 > mailto:lsettimo@abo.fi > http://www.abo.fi/~lsettimo
participants (3)
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Andrej Sali -
fisera -
Luca Settimo