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PostPosted: Sun Aug 09, 2009 9:56 am 
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Hi,

Does anyone happens to know whether is possible to fix (translation wise) atoms of the ligand whilst keep the torsions free?

Many thanks,

Eucaria


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PostPosted: Sun Aug 09, 2009 11:34 pm 
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If you mean keeping the molecule center fixed and suppressing rotation about that point, I think you should be able to do this with a simulated annealing search. Set the initial position and quaternion with the tran0 and quat0 keywords in the dpf. Then set tstep and qstep to zero (I haven't tried this - I believe you can set them to zero but perhaps you'll have to set them to some very small positive number instead). This won't work with a GA search since you start with a randomized population - specifying a ligand conformation with tran0 and quat0 etc. in this case only seeds the population with one member having that conformation, the rest being randomized.

In version 4.2, I believe you might be able to do something similar with a psuedo-Solis&Wets local search by setting psw_trans_scale and psw_rot_scale to zero.

Hope this helps.

Regards,

Mark


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