hetatms placed far away from the backbone
Dear Modellers, I'm trying to model a ZN-containing (two zn ions) protein with modeller6v2. I used : 'SET HETATM_IO = on' in the .top file and the following syntax in the .ali file : ------------------------------------------ >P1;template structure:template:2:A: :A: : : : ANHD...VGN---LYPE-/zz* >P1;target sequence:target: : : : : : : : ANHD...VGNPL-LYR-G/zz* --------------------------------------------- I renamed the ZN in the template pdb file to ZN2 and the residue numbers are continuous. The model building results in a model where the overall structure of the model looks almost good, but the zn atoms are PLACED FAR AWAY from the model backbone. I tried to solve this problem many times without success so far. So, I would be very happy if anybody could help me. Thanks to all in advance, Michael ******************************************** Michael Knoll email : michael.knoll@itb.uni-stuttgart.de ********************************************
On Wed, Oct 13, 2004 at 04:23:10PM +0200, Michael Knoll wrote: > I'm trying to model a ZN-containing (two zn ions) protein with > modeller6v2. ... > The model building results in a model where the overall structure of the > model looks almost good, but the zn atoms are PLACED FAR AWAY from the > model backbone. Modeller may not be able to guess which restraints you need between your hetatoms (Zn) and neighboring residues - you can check the restraints file generated during modeling to see if any restraints were defined on the Zn atoms. Most likely, you will have to add some user-defined restraints to keep the geometry of the Zn-binding site. See, for example, the tutorial for a similar system at http://salilab.org/modeller/methenz/ The text for example 2 can be found at: http://salilab.org/modeller/methenz/andras/node16.html (The text applies to a rather old version of Modeller, but the example TOP files, at ftp://salilab.org/tutorials/methenz/example2/, will work with Modeller 7v7, and probably 6v2.) Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage
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