Dear modellers, dear Andej Sali,
I have one question for you. I built several protein models using modeller 4 time ago... I used in the top file the following parameters:
SET HETATM_IO = on and off SET WATER_IO = on and off SET HYDROGEN_IO = off SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 SET MD_LEVEL = 'refine3' CALL ROUTINE = 'model' and I build the model with and without ligand and water in the binding site...
since the models that I built are quite a lot my question is:
do I have to expect some difference with the models obtained using the new version (modeller 6 released the 25 January 2002) ... or do I have to expect the same result? for example does something differ when I model the ligand in the two version? or just by using the same parameter in the top file above here?
Thanks
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