Checking for Correct Optimized Structure

[GJK]

Dear Mr.Nordland,

Here is the file.

Thanks in advance

[GJK]

Dear sir,

Kindly reply.I am waiting eagerly to confirm my results.

[Anders Blom]

Can you restate your actual question, I think it got lost a bit in the back-and-forths.

[GJK]

Dear Mr.Anders Blom,

I optimized the structure of drug methotrexate got from chemspider as advised by Mr.Nordland.I attached the .py file in my previous mail as Mr.Nordland asked me,to give his confirmation about the optimized drug Methotrexate.

I am waiting for the same.I could not attach the.nc file due to the large file size not accepted in the forum.If u want that file too kindly give me an alternate mail id.

Thanks in advance

[Anders Blom]

As I understood the original discussion, it was a matter of using DZP vs SZ basis set, and how to assess the difference in two configurations. SZ is probably a bit simplistic, but if you used DZP, the results are correct on that level of approximation provided the forces converged to your requested tolerance (and your input is reasonable). Beyond that, the responsibility is yours to account for the scientific validity of your calculations.

[GJK]

thank you

But i converted the structure to ATK compatible format after downloading from chemspider.

The doubt was whether my optimized result is correct since my system hanged after optimization.If u could provide me with your alternate mail id I can send u the .nc file my mail id is nanojananik@gmail.com

[Anders Blom]

I don't think anyone can say if the structure is "correct" or not by just looking at it, in a file or image, doesn't matter. One needs to know exactly how the simulation was carried out, when it crashed, which files you have, etc, etc. If the structure was optimized to the end then you have an optimized structure. If it crashed and you only have the last image in a trajectory or checkpoint file, then it's probably not relaxed. If you are unsure, compute the forces on all atoms in the resulting structure. And in the end, if you suspect the structure is not correct, why not just rerun the optimization? Surely that's faster than waiting days for an answer to a question nobody can answer.

[Shinji Usui]

If you want to find a global minimum configuration for a drug like organic compound, just relaxing the structure from
one initial structure is not enough.   Because the structure may lie in a local minimum by the optimization procedure.
It is depend on which structure you chose as an initial structure.

You should find a global minimum conformation of the compound, and this method is called "conformational search".
(Please search the word by google)

There are several methods of conformational search, general one will be
1.  Find rotatable dihedral bonds in the system.  
2.  Generate the all structures by changing the values of the dihedral angles in the system
3.  Optimize all structures and calculate total energies
4.  The structure which has a minimum energy is global minimum configuration.

We hope you find it informative.