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alex
yakovenko.alexander@gmail.com

Alex


On Tue Aug 5 '14 11:25pm, Alex Granovsky wrote
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>Dear Alex,

>It is possible to do this with Firefly. You need to use DLC
>coordinates, then you will be able to freeze internals using
>ifzmat array of $zmat and freeze atoms using ifreez array of
>$statpt. Note: to freeze atoms 1 and 2, use: ifreez(1)=1,2,3, 4,5,6

>Hope this helps.

>Kind regards,
>Alex Granovsky

>P.S. There exist an alternative method of freezing atoms with DLCs
>namely using IFRZAT array. I do not describe it here because it is
>less suitable for freezing a large number of internals.
>
>
>
>
>On Sun Aug 3 '14 2:06am, alex wrote
>-----------------------------------
>>Dear colleagues,
>>I am wondering about constraints with firefly. I am modeling/screening a catalytic reaction of my enzyme as a function of small synthetic cofactors. The approach is DFT supermolecular cluster of c.a. 200 atoms that represents the catalytic site; a small subset of the system is the variable (cofactor). Besides,there is a substrate, metal and oxygen molecules (the reaction is oxidation). My current problem is that firefly applies constraints in internal or Cartesian coordinates with either/or logic. I wish it is possible to freeze some atoms (CA of protein residues) in Cartesian coordinates (to represent the rest of the protein body implicitly) but constrain the distance between the oxygen and the substrate in internal coordinates (as a distance). Is there any way to make such constraints in firefly? Or maybe there is software to automatically construct a tractable z-matrix like description for big systems which consists of many separated fragments with some frozen atoms?
>>Thanks,
>>Alex
>>