QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: GJK on January 13, 2014, 06:23
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Dear all,
I have attached the .jpeg file of Methotrexate drug before(initial) and after(final) optimization.
Kindly help me whether my structure is correct according to the structure given by DRUG BANK.
If the optimization is correct i will move on to the convergence studies for total energy for k point sampling.
The structure converged in 123 steps and density mesh cut-off-150 Ry K points (1 1 300)
I have attached the .xyz file format of the drug converted using open babel as it was in .mol format from the DRUG BANK.
Regards
Janani.K
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Looks like there is something wrong with the initial structure. Not completely (atomic units?)
The structure you can find here http://www.chemspider.com/Chemical-Structure.112728.html (http://www.chemspider.com/Chemical-Structure.112728.html) looks fine.
Attached you can find the .xyz format converted with openbabel.
You can optimize the structure in a molecular configuration meaning also that you do not need k-points (1,1,1)
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Thank you.
I understood the mistake. But cannot sort it out.
In open babel I fixed the parameters as add hydrogens (make explicit) and generate 3D coordinates.But the structure which I generated is not accurate with the one which you have sent correctly.Kindly help me what are the other parameters to be fixed in open babel while converting the .mol file to .xyz format.
I have attached the .jpeg file of the structure converted with above mentioned parameters.
Janani.K
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I did not use any extra parameters.
The .MOL file that you download from chemspider.com has already the H atoms included :)
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I have attached the .xyz file and MDL MOL file downloaded from chemspider it has no hydrogen atoms when i insert the file in open babel for conversion.When add hydrogens(explicit) and generate 3D coordinates cheque boxes are clicked 55 atoms of Methotrexate structure is generated but the structure is not exact with the same as u mailed me.Kindly help in sorting out this problem.
open bable input-MDL mol file
33 35 0 0001 0 0 0 0 0999 V2000
2.1434 -4.5375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
2.8579 -4.9500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0
2.8579 -5.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
2.1434 -6.1875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
2.1434 -7.0125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
1.4289 -7.4250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0
0.7145 -7.0125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
0.0000 -7.4250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0
-0.7145 -7.0125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
-1.4289 -7.4250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0
-0.7145 -6.1875 0.0000 N 0 0 0 0 0 0 0 0 0 0 0
0.0000 -5.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
0.0000 -4.9500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0
0.7145 -6.1875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
1.4289 -5.7750 0.0000 N 0 0 0 0 0 0 0 0 0 0 0
3.5724 -4.5375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
3.5724 -3.7125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
4.2868 -3.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
5.0013 -3.7125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
5.0013 -4.5375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
4.2868 -4.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
5.7158 -3.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
5.7158 -2.4750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0
6.4302 -3.7125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0
7.1447 -3.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
7.8592 -3.7125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
8.5737 -3.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
9.2881 -3.7125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
10.0026 -3.3000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0
9.2881 -4.5375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0
7.1447 -2.4750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
7.8592 -2.0625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0
6.4302 -2.0625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
4 5 2 0
5 6 1 0
6 7 2 0
7 8 1 0
8 9 2 0
9 10 1 0
9 11 1 0
11 12 2 0
12 13 1 0
12 14 1 0
7 14 1 0
14 15 2 0
4 15 1 0
2 16 1 0
16 17 2 0
17 18 1 0
18 19 2 0
19 20 1 0
20 21 2 0
16 21 1 0
19 22 1 0
22 23 2 0
22 24 1 0
25 24 1 6
25 26 1 0
26 27 1 0
27 28 1 0
28 29 1 0
28 30 2 0
25 31 1 0
31 32 1 0
31 33 2 0
M END
> <StdInChI>
InChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)/t13-/m0/s1
> <StdInChIKey>
FBOZXECLQNJBKD-ZDUSSCGKSA-N
> <AuxInfo>
1/1/N:1,18,20,17,21,26,27,5,3,19,4,16,25,28,14,12,7,22,31,9,13,10,6,15,24,11,8,2,29,30,23,32,33/E:(2,3)(4,5)(29,30)(32,33)/it:im/rA:33nCNCCCNCNCNNCNCNCCCCCCCONCCCCOOCOO/rB:s1;s2;s3;d4;s5;d6;s7;d8;s9;s9;d11;s12;s7s12;s4d14;s2;d16;s17;d18;s19;s16d20;s19;d22;s22;n24;s25;s26;s27;s28;d28;s25;s31;d31;/rC:2.1434,-4.5375,0;2.8579,-4.95,0;2.8579,-5.775,0;2.1434,-6.1875,0;2.1434,-7.0125,0;1.4289,-7.425,0;.7145,-7.0125,0;0,-7.425,0;-.7145,-7.0125,0;-1.4289,-7.425,0;-.7145,-6.1875,0;0,-5.775,0;0,-4.95,0;.7145,-6.1875,0;1.4289,-5.775,0;3.5724,-4.5375,0;3.5724,-3.7125,0;4.2868,-3.3,0;5.0013,-3.7125,0;5.0013,-4.5375,0;4.2868,-4.95,0;5.7158,-3.3,0;5.7158,-2.475,0;6.4302,-3.7125,0;7.1447,-3.3,0;7.8592,-3.7125,0;8.5737,-3.3,0;9.2881,-3.7125,0;10.0026,-3.3,0;9.2881,-4.5375,0;7.1447,-2.475,0;7.8592,-2.0625,0;6.4302,-2.0625,0;
> <Formula>
C20 H22 N8 O5
> <Mw>
454.4393
> <SMILES>
CN(C1C=CC(C(N[C@H](C(=O)O)CCC(=O)O)=O)=CC=1)CC1N=C2C(N=C(N=C2N)N)=NC=1 |&1:8|
> <CSID>
112728
$$$$
open babel output-xyz file
55
C 1.04381 0.04587 -0.07731
N 2.47831 0.04587 -0.07731
C 3.19556 -0.58808 0.99108
C 2.23250 -1.16290 1.95980
C 4.38993 -2.55496 4.30580
N 3.54596 -3.05870 5.15474
C 2.26908 -2.93759 4.95064
N 1.42511 -3.44133 5.79959
C 1.85802 -4.06618 6.85263
N 3.23101 -4.19640 7.07208
N 1.01406 -4.56992 7.70157
C 0.50114 -2.16626 3.65075
N 0.03564 -1.49438 2.51845
C 1.82145 -2.29149 3.86179
N 2.66541 -1.78775 3.01284
C 3.17656 0.66303 -1.11739
C 6.53386 0.06955 -0.11721
C 7.20532 0.66303 -1.11739
C 6.53386 1.25651 -2.11757
C 5.19094 1.25651 -2.11757
C 4.51948 0.66303 -1.11739
C 7.25586 1.89467 -3.19303
O 6.64206 2.43718 -4.10731
N 8.65236 1.89467 -3.19303
C 9.36961 2.52862 -4.26141
C 9.00240 4.00268 -4.31356
C 7.50800 4.14441 -4.55243
C 7.14997 5.58161 -4.60326
O 8.10551 6.52074 -4.44584
O 5.98387 5.91749 -4.78863
C 10.82665 2.39042 -4.02852
O 11.27631 1.74140 -2.93473
O 11.62438 2.86657 -4.83095
H 0.68714 -0.46892 0.79026
H 0.68714 -0.44807 -0.95692
H 0.68714 1.05461 -0.06527
H 3.81071 0.13433 1.48565
H 3.81072 -1.36834 0.59400
H 5.42174 -2.56502 4.32276
H 3.87077 -3.81455 6.42855
H 3.55917 -4.67006 7.87033
H -0.93228 -1.40258 2.36373
H 0.67540 -1.11253 1.87491
H 6.89437 -0.42390 0.71439
H 8.23732 0.66303 -1.11739
H 4.67494 1.71259 -2.88618
H 5.03548 0.20696 -0.34878
H 9.14461 1.45958 -2.45980
H 9.11111 2.06361 -5.18977
H 9.53741 4.47555 -5.11047
H 9.26089 4.46769 -3.38520
H 6.97299 3.67154 -3.75551
H 7.24951 3.67939 -5.48078
H 7.87915 7.42942 -4.47798
H 12.19754 1.65402 -2.78748
Thanks in Advance
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Click on the 3D view (Jmol applet) before saving the file.
Here the two files.
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Thank you.
Just clarify whether this structure is correct.
I clicked on 3D and then click save and got the 55 atoms.
Kindly give your confirmation if the attached structure is correct.
Janani.K
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One more doubt
I chose density mesh cut-off-150 Ry(default) and Single zeta polarised-Basis set
Is that ok for optimization?
or the parameters mentioned above has to be changed for drugs.
But as default for this drug double zeta polarised basis set is available which I changed to reduce computational timing.
Kindly clarify
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With a system of this size, I would try with DZP first and then I would perform the same relaxation with SZ, and if the structures were close enough, I would continue with SZ.
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With a system of this size, I would try with DZP first and then I would perform the same relaxation with SZ, and if the structures were close enough, I would continue with SZ.
How to confirm that the structures are close enough after doing optimization with DZP nad SZ
What are the parameters that describe the closeness of the structure.
Kindly confirm me whether the structure which I attached after getting the procedure from Mr.Umberto Martinez is correct.
Thanks
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Dear Mr.Nordland,
Kindly clarify the quote mentioned below.
With a system of this size, I would try with DZP first and then I would perform the same relaxation with SZ, and if the structures were close enough, I would continue with SZ.
How to confirm that the structures are close enough after doing optimization with DZP nad SZ
What are the parameters that describe the closeness of the structure.
Kindly confirm me whether the structure which I attached after getting the procedure from Mr.Umberto Martinez is correct.
Thanks
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Dear Mr.Nordland,
Comming back again after optimizing the structure.
I have attached the files and jpeg image of optimized structure of drug methotrexate after your advice.Kindly give your approval if it is correct.I used DZP for optimization using DFT.
But sir my system hanged so I shut down and restarted I found that the optimization had finished before.This will not create any problem know? Will the system hang after finishing a long calculation
Waiting for your approval.
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The system shouldn't not hang after a long calculation.
-However I can't approve your systems by looking at screenshot, I will the coordinates obtained by relaxing with both methods.
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Dear Mr.Nordland,
I attached the file but the size was larger than the limit in the forum.So I couldn't attach.
Kindly give me an alternative mail ID to send the files sir.
Thank you.
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Dear Mr.Nordland,
I attached the file but the size was larger than the limit in the forum.So I couldn't attach.
Kindly give me an alternative mail ID to send the files sir.
Thank you.
Just attached the python scripts to this post.
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Dear Mr.Nordland,
Here is the file.
Thanks in advance
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Dear sir,
Kindly reply.I am waiting eagerly to confirm my results.
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Can you restate your actual question, I think it got lost a bit in the back-and-forths.
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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
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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.
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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
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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.
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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.