I am trying to find the reaction pathway of an enzymatic reaction using the QST2 keyword in Gaussian.
I am modeling the active site with the two amino acid residues identified to be taking part in the reaction and fixing some of the atoms in the amino acid backbone to make sure freedom to move is limited (as in the case of Enzyme).
I did this by using Cartesian co-ordinates input and freezing individual atoms (by inserting -1 in front of the atoms I need to freeze). I have optimized both the reactant and expected product structures this way.
In the reactant and product structures, the fixed atoms have different cartesian co-ordinates. However, bond distances between the fixed atoms in the structures remain the same.
Due to this change in co-ordinates (As I have assumed), there comes an error in the internal co-ordinate system when I try to do the QST2 calculation.
Is there a way to solve this issue? I have attached the QST2 input file.
Dear,
I can understand the difficulty as there are no guarantees of finding the right TS even after so many attempts.
First, be sure that what you have optimized is right structure of reactant and expected product, by running frequence calculation.
Also, pay attention to the gaussian technical note http://gaussian.com/qst2/
Good luck
First - make sure to freeze the positions of as little atoms as possible. One per amino acid is usually enough; the more you freeze, the more unrealistic the system becomes.
Secondly - it's probably a good idea to freeze the same atoms in the reactants and products and freeze them at the same positions.
Thirdly - step two obviously limits the flexibility and movement of amino acid residues. If you expect large changes of these residues during reaction, then you should probably add to the system 1 neighboring residue and freeze atoms in the other residue, so the crucial residue is fully flexible.
Dear Bartosz, Athar:
I have frozen the same atoms in the reactant and product and have used the same numbers for the atoms. The problem arises because even though the bond lengths and angles of the fixed atoms of reactant and products are the same, their cartesian coordinates are drastically different.
Thank you for your kind attention.
Dilhan
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