Closed whe280 closed 3 years ago
KristapsE
commented
3 years ago Hi, what do the *.tout files look like? To me it looks like TINKER launches, but doesn't finish correctly. Have you tried running TINKER manually outside the script? Did you download the mmff.prm file from the TINKER website?
whe280
commented
3 years ago Hi,Thank you for your prompt reply.I haven't tried running TINKER manually outside the script.I downloaded Tinker8 at https://github.com/TinkerTools/tinker and compiled source code. mmff.prm file is also from the above website.The content of *.tout file is as follows.
################################################################################################################################################
########################################################################## ######################################################################
Enter Potential Parameter File Name :
Additional Partial Charges for Specific Atoms :
Atom Charge
1 -0.2882
2 0.1382
3 0.2800
4 0.1382
5 -0.2882
6 0.0000
7 0.0000
8 0.0000
9 0.0000
10 0.1500
11 0.1500
12 0.0000
13 0.0000
14 0.0000
15 0.0000
16 -0.6800
17 0.4000Number of Torsions Used in Derivative Computation : 2
Enter RMS Gradient per Atom Criterion [0.0001] :
Generating Seed Point for Potential Energy Surface Scan
Potential Surface Map Minimum 1 100000.0000Normal Mode Local Search Minimum 1
Search Direction 1 >>>>>>
Search Direction 2 >>>>>>
Search Direction 3 >>>>>>
Search Direction 4 >>>>>>For the *.tout files , please see attached release notes.Really appreciate your help! Look forward to your reply.
On 1/4/2021 23:12，KristapsEnotifications@github.com wrote：
Hi, what do the *.tout files look like? To me it looks like TINKER launches, but doesn't finish correctly. Have you tried running TINKER manually outside the script? Did you download the mmff.prm file from the TINKER website?
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.
KristapsE
commented
3 years ago This seems to be closely connected, perhaps identical issue to #36. A patch to be copied over the RunTinker function in Tinker.py has been suggested by @gkxiao . I haven't had time to properly test it on my end, so I haven't yet incorporated in the main branch, but feel free to try and see if it resolves the issue.
whe280
commented
3 years ago Really appreciate your reply!With reference of the opinion from @gkxiao ,I modified the RunTinker function in Tinker.py.The content of *.tout file is as follows.
################################################################################################################################################
########################################################################## ######################################################################
Additional Partial Charges for Specific Atoms :
Atom Charge
1 -0.2882
2 0.1382
3 0.2800
4 0.1382
5 -0.2882
6 0.0000
7 0.0000
8 0.0000
9 0.0000
10 0.1500
11 0.1500
12 0.0000
13 0.0000
14 0.0000
15 0.0000
16 -0.6800
17 0.4000Number of Torsions Used in Derivative Computation : 2
Generating Seed Point for Potential Energy Surface Scan
Potential Surface Map Minimum 1 100000.0000Normal Mode Local Search Minimum 1
Search Direction 1 >>>>>>
Search Direction 2 >>>>>>
Search Direction 3 >>>>>>
Search Direction 4 >>>>>>On 1/5/2021 20:20，KristapsEnotifications@github.com wrote：
This seems to be closely connected, perhaps identical issue to #36. A patch to be copied over the RunTinker function in Tinker.py has been suggested by @gkxiao . I haven't had time to properly test it on my end, so I haven't yet incorporated in the main branch, but feel free to try and see if it resolves the issue.
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KristapsE
commented
3 years ago In that case it might be connected with the particular molecule, which is very rigid and it might be that TINKER is unable to find any conformers at all. Perhaps try with one of the slightly more flexible ones from the test set, like AT3?
whe280
commented
3 years ago Thanks a lot! According to your suggestion,I tried with AT3 . The command I used was: python3 PyDP4.py -s chloroform -w gmns -m t -f mmff AT3_.sdf NMR_folder
========================== PyDP4 script, integrating Tinker/MacroModel, Gaussian/NWChem and DP4 v1.0
Settings read from settings.cfg: SCHRODINGER: TinkerPath: /home/node0/work/whe/tinker NWChemPath: nwchem GausPath: g16 ['AT3_.sdf'] NMR_folder NMR_path /home/node0/work/whe/DP4-AI-master/NMRfolder Current working directory: /home/node0/work/whe/DP4-AI-master Initial input files: ['AT3.sdf'] NMR file: [PosixPath('/home/node0/work/whe/DP4-AI-master/NMR_folder/Carbon'), PosixPath('/home/node0/work/whe/DP4-AI-master/NMR_folder/Proton')] Workflow: gmns
Generating diastereomers... Getting inchi from file AT3.sdf Getting inchi from file AT3.sdf Number of diastereomers to be generated: 2 Isomer 0 inchi = InChI=1S/C13H19F2NO/c1-3-13(9(2)8-17)16-7-10-11(14)5-4-6-12(10)15/h4-6,9,13,16-17H,3,7-8H2,1-2H3/t9-,13+/m0/s1/f/ Isomer 1 inchi = InChI=1S/C13H19F2NO/c1-3-13(9(2)8-17)16-7-10-11(14)5-4-6-12(10)15/h4-6,9,13,16-17H,3,7-8H2,1-2H3/t9-,13-/m0/s1/f/ Generated input files: ['AT3_1', 'AT3_2']
Assuming all computations are done? ... False Using preexisting DFT data? ... False Performing conformational search using Tinker
Setting up Tinker files... Tinker input for AT3_1 prepared. Tinker input for AT3_2 prepared.
Running Tinker...
/home/node0/work/whe/tinker/bin/scan AT3_1 /home/node0/work/whe/tinker/params/mmff.prm 0 10 20 0.00001 | tee ./AT3_1.tout
Tinker job 1 of 2 completed.
/home/node0/work/whe/tinker/bin/scan AT3_2 /home/node0/work/whe/tinker/params/mmff.prm 0 10 20 0.00001 | tee ./AT3_2.tout
Tinker job 2 of 2 completed.
AT3_1 is matching conformational search output for AT3_1
Reading AT3_1
Traceback (most recent call last):
File "PyDP4.py", line 718, in
The content of *.tout file is as follows.
################################################################################################################################################
########################################################################## ######################################################################
Additional Partial Charges for Specific Atoms :
Atom Charge
1 0.0000
2 0.0000
3 0.2700
4 0.0000
5 0.2800
6 -0.6800
7 -0.9000
8 0.4135
9 -0.1500
10 -0.1500
11 0.1900
12 -0.1435
13 0.1900
14 -0.1500
15 0.1500
16 0.1500
17 0.1500
18 -0.1900
19 -0.1900
20 0.0000
21 0.0000
22 0.0000
23 0.0000
24 0.0000
25 0.0000
26 0.0000
27 0.0000
28 0.4000
29 0.0000
30 0.0000
31 0.0000
32 0.0000
33 0.0000
34 0.0000
35 0.0000
36 0.3600INITROT -- Rotation about 8 7 occurs more than once in Z-matrix
Tinker is Unable to Continue; Terminating the Current Calculation
On 1/5/2021 21:35，KristapsEnotifications@github.com wrote：
In that case it might be connected with the particular molecule, which is very rigid and it might be that TINKER is unable to find any conformers at all. Perhaps try with one of the slightly more flexible ones from the test set, like AT3?
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KristapsE
commented
3 years ago This seems like a bug in TINKER. According to this link, the atoms need to be renumbered in the input file:| INITROT -- Rotation about 8 7 occurs more than once in Z-matrix
DP4-AI includes a utility TreeRenum.py, which I wrote 5 years ago when encountering similar problems with TINKER. I have not used it in a while, but you might try renumbering AT3.sdf with that and then try again. It usually resolved TINKER issues back then.
whe280
commented
3 years ago Hello, Thank you for your suggestion, and I am very sorry that I did not reply to your message in time due to going out for the exam. this is the result of running the code.May I ask if I did something incorrectly
The following is the content of AT3r.sdf ,which was renumbered by AT3.sdf using the TreeRenumSDF function inTreeRenum.py.
OpenBabel01072109163D
36 35 0 0 1 0 0 0 0 0999 V2000 -4.6167 4.0212 0.7531 F 0 0 0 0 0 0 0 0 0 0 0 0 -5.4903 3.4592 1.6250 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8629 3.4439 1.3097 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7891 2.8701 2.2023 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3403 2.3203 3.4187 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9691 2.3417 3.7405 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0339 2.9026 2.8409 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5573 2.9309 3.1981 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9374 1.6079 3.2162 N 0 0 0 0 0 2 0 0 0 0 0 0 -2.1774 1.2670 2.0151 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6663 1.2396 2.4012 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1103 2.6678 2.5988 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1870 2.6359 3.1638 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7703 2.1786 2.5761 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2060 3.8755 0.3788 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8409 2.8518 1.9600 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0407 1.8831 4.1146 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5595 1.8316 4.9266 F 0 0 0 0 0 0 0 0 0 0 0 0 -3.0147 3.6196 2.5471 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4830 3.3499 4.2028 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1665 1.2922 3.2161 H 0 0 0 0 0 15 0 0 0 0 0 0 -2.7297 -0.0882 1.5191 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1995 -0.0326 1.0785 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5128 -0.9846 0.6511 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3451 2.0020 1.2261 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5707 0.7016 3.3465 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2079 0.4809 1.3820 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2633 0.5206 1.6491 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7415 3.2394 3.2794 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0911 3.2098 1.6517 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1603 -0.4295 0.6550 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6071 -0.8526 2.2879 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8540 0.1774 1.9238 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3578 0.7420 0.3280 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0465 -0.5779 1.3445 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1009 0.8923 0.3785 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 7 1 0 0 0 0 3 2 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 17 1 0 0 0 0 6 18 1 0 0 0 0 7 8 1 0 0 0 0 7 6 2 0 0 0 0 8 9 1 0 0 0 0 8 20 1 0 0 0 0 10 25 1 6 0 0 0 10 11 1 0 0 0 0 10 9 1 0 0 0 0 11 12 1 0 0 0 0 11 26 1 1 0 0 0 12 13 1 0 0 0 0 12 29 1 0 0 0 0 14 13 1 0 0 0 0 15 3 1 0 0 0 0 16 4 1 0 0 0 0 19 8 1 0 0 0 0 22 10 1 0 0 0 0 22 32 1 0 0 0 0 23 22 1 0 0 0 0 23 33 1 0 0 0 0 24 23 1 0 0 0 0 27 28 1 0 0 0 0 27 11 1 0 0 0 0 30 12 1 0 0 0 0 31 22 1 0 0 0 0 34 23 1 0 0 0 0 35 27 1 0 0 0 0 36 27 1 0 0 0 0 M END $$$$
On 1/5/2021 22:14，KristapsEnotifications@github.com wrote：
This seems like a bug in TINKER. According to this link, the atoms need to be renumbered in the input file:| INITROT -- Rotation about 8 7 occurs more than once in Z-matrix
DP4-AI includes a utility TreeRenum.py, which I wrote 5 years ago when encountering similar problems with TINKER. I have not used it in a while, but you might try renumbering AT3.sdf with that and then try again. It usually resolved TINKER issues back then.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.
KristapsE
commented
3 years ago So the TreeRenum.py will not run the DP4-AI process itself. Its only purpose is to prepare an sdf file that TINKER likes better. I would suggest you renumber the input file with this (as you have already done), and then try the DP4-AI script again with the renumbered sdf, instead of the original.
whe280
commented
3 years ago I tried the DP4-AI script again with the renumbered sdf.The renumbered sdf seems to have some problems running in InchiGen.py. I tried my best to check it for a while, but due to poor programming ability, I didn’t find the reason.
The command I used was:
python3 PyDP4.py -s chloroform -w gmns -m t -f mmff AT3_r.sdf NMR_folder
The result was:
Generating diastereomers... Getting inchi from file AT3_r.sdf [19:39:29] WARNING: Accepted unusual valence(s): N(2) Getting inchi from file AT3_r.sdf [19:39:29] WARNING: Accepted unusual valence(s): N(2) Number of diastereomers to be generated: 4 Traceback (most recent call last): File "PyDP4.py", line 718, in <module> main(settings) File "PyDP4.py", line 188, in main settings.InputFiles = InchiGen.GenDiastereomers(settings.InputFiles[0], settings.SelectedStereocentres) File "/home/node0/work/whe/DP4-AI-master/InchiGen.py", line 306, in GenDiastereomers ds_inchis = [FixTautProtons(f, i, aux) for i in ds_inchis] File "/home/node0/work/whe/DP4-AI-master/InchiGen.py", line 306, in <listcomp> ds_inchis = [FixTautProtons(f, i, aux) for i in ds_inchis] File "/home/node0/work/whe/DP4-AI-master/InchiGen.py", line 53, in FixTautProtons amap = GetInchiRenumMap(AuxInfo) File "/home/node0/work/whe/DP4-AI-master/InchiGen.py", line 45, in GetInchiRenumMap amap = [int(x) for x in RenumLayer[2:].split(',')] File "/home/node0/work/whe/DP4-AI-master/InchiGen.py", line 45, in <listcomp> amap = [int(x) for x in RenumLayer[2:].split(',')] ValueError: invalid literal for int() with base 10: '13;21'
KristapsE
commented
3 years ago Have you tried looking at the starting sdf and the resulting sdf with Avogadro or jmol or similar? The differences, if any, might provide clues as to what is going wrong.
You could also try skipping the diastereomer generation for now. Just renumber the AT3_1.sdf, AT3_2.sdf etc, and then submit them to PyDP4.py using python3 PyDP4.py -s chloroform -w mns -m t -f mmff AT3_1r.sdf AT3_2r.sdf NMR_folder
gkxiao
commented
3 years ago If you re-prepare the AT3.sdf and replace the original one, it works. Here is the AT3.sdf file I used.
AT3
Mrv2008 01072123113D
36 36 0 0 0 0 999 V2000
-0.0166 -0.9858 -2.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2070 -1.2272 -3.9255 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3256 -0.1533 -4.8203 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2619 1.1646 -4.3424 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0767 1.4134 -2.9680 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0597 0.3414 -2.0470 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0803 -2.0288 -1.7688 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.0350 2.6600 -2.5763 F 0 0 0 0 0 0 0 0 0 0 0 0
0.2819 0.6063 -0.5949 C 0 0 1 0 0 0 0 0 0 0 0 0
-1.0100 0.9025 0.0782 N 0 0 2 0 0 0 0 0 0 0 0 0
-1.0442 1.0602 1.5661 C 0 0 2 0 0 0 0 0 0 0 0 0
-0.2827 2.3591 2.0006 C 0 0 1 0 0 0 0 0 0 0 0 0
-0.6427 -0.2454 2.3653 C 0 0 1 0 0 0 0 0 0 0 0 0
-0.7662 3.6633 1.3226 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5989 -0.0430 3.9106 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5755 -1.4625 2.0705 C 0 0 2 0 0 0 0 0 0 0 0 0
-1.5673 -1.8463 0.7024 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.2618 -2.1855 -4.2795 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.4605 -0.3306 -5.8173 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3540 1.9428 -4.9997 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7690 -0.2534 -0.1389 H 0 0 0 0 0 0 0 0 0 0 0 0
0.9655 1.4469 -0.4687 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.6658 0.1614 -0.1691 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.0965 1.2444 1.7996 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.4216 2.5266 3.0694 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7884 2.2426 1.8210 H 0 0 0 0 0 0 0 0 0 0 0 0
0.3667 -0.5349 2.0708 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6194 3.6210 0.2433 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.8242 3.8313 1.5356 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.1988 4.5130 1.7142 H 0 0 0 0 0 0 0 0 0 0 0 0
0.2034 0.6376 4.1924 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.5498 0.3566 4.2681 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.4001 -0.9842 4.4277 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.6016 -1.2276 2.3606 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2567 -2.3405 2.6409 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2487 -2.5476 0.6314 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
4 5 2 0 0 0 0
5 6 1 0 0 0 0
1 6 2 0 0 0 0
1 7 1 0 0 0 0
5 8 1 0 0 0 0
6 9 1 0 0 0 0
9 10 1 0 0 0 0
11 10 1 0 0 0 0
11 12 1 0 0 0 0
11 13 1 0 0 0 0
12 14 1 0 0 0 0
13 15 1 0 0 0 0
13 16 1 0 0 0 0
16 17 1 0 0 0 0
2 18 1 0 0 0 0
3 19 1 0 0 0 0
4 20 1 0 0 0 0
9 21 1 0 0 0 0
9 22 1 0 0 0 0
10 23 1 0 0 0 0
11 24 1 0 0 0 0
12 25 1 0 0 0 0
12 26 1 0 0 0 0
13 27 1 0 0 0 0
14 28 1 0 0 0 0
14 29 1 0 0 0 0
14 30 1 0 0 0 0
15 31 1 0 0 0 0
15 32 1 0 0 0 0
15 33 1 0 0 0 0
16 34 1 0 0 0 0
16 35 1 0 0 0 0
17 36 1 0 0 0 0
M END
$$$$
And then type the command line:
PyDP4.py -s chloroform -w gmns -m t -f mmff AT3_.sdf NMR_folder
It works well. Here is the first 100 lines:
(/home/cloudam/rdkit2020) [cloudam@master AT3]$ head -100 AT3_1.tout
######################################################################
##########################################################################
### ###
### Tinker --- Software Tools for Molecular Design ###
## ##
## Version 8.8 June 2020 ##
## ##
## Copyright (c) Jay William Ponder 1990-2020 ##
### All Rights Reserved ###
### ###
##########################################################################
######################################################################
Additional Partial Charges for Specific Atoms :
Atom Charge
1 0.1900
2 -0.1500
3 -0.1500
4 -0.1500
5 0.1900
6 -0.1435
7 -0.1900
8 -0.1900
9 0.4135
10 -0.9000
11 0.2700
12 0.0000
13 0.0000
14 0.0000
15 0.0000
16 0.2800
17 -0.6800
18 0.1500
19 0.1500
20 0.1500
21 0.0000
22 0.0000
23 0.3600
24 0.0000
25 0.0000
26 0.0000
27 0.0000
28 0.0000
29 0.0000
30 0.0000
31 0.0000
32 0.0000
33 0.0000
34 0.0000
35 0.0000
36 0.4000
Number of Torsions Used in Derivative Computation : 9
Generating Seed Point for Potential Energy Surface Scan
Potential Surface Map Minimum 1 15.3984
Normal Mode Local Search Minimum 1
Search Direction 1 Step 17 12.0420
Potential Surface Map Minimum 2 12.0420
Search Direction 2 Step 31 15.6659
Potential Surface Map Minimum 3 15.6659
Search Direction 3 Step 20 14.6114
Potential Surface Map Minimum 4 14.6114
Search Direction 4 Step 31 10.5926
Potential Surface Map Minimum 5 10.5926
Search Direction 5 Step 24 13.5561
Potential Surface Map Minimum 6 13.5561
Search Direction 6 Step 41 19.1721
Potential Surface Map Minimum 7 19.1721
Search Direction 7 Step 19 18.3819
Potential Surface Map Minimum 8 18.3819
Search Direction 8 Step 22 16.3829
Potential Surface Map Minimum 9 16.3829
Search Direction 9 Step 35 15.8690
And here is the last 50 lines：
(/home/cloudam/rdkit2020) [cloudam@master AT3]$ tail -50 AT3_1.tout
Search Direction 1 Step 18 11.0880
Search Direction 2 Step 15 22.3189
Search Direction 3 Step 20 19.1814
Search Direction 4 Step 28 11.2383
Search Direction 5 Step 29 14.2571
Search Direction 6 Step 23 13.2098
Search Direction 7 ------
Search Direction 8 Step 11 17.2300
Search Direction 9 Step 19 16.0223
Search Direction 10 Step 31 14.0340
Normal Mode Local Search Minimum 1274
Search Direction 1 Step 12 17.9563
Search Direction 2 Step 19 12.7673
Search Direction 3 Step 21 14.4921
Search Direction 4 Step 10 14.8935
Search Direction 5 Step 31 17.0459
Search Direction 6 Step 49 22.0807
Search Direction 7 ------
Search Direction 8 Step 46 13.2581
Search Direction 9 Step 40 15.3224
Search Direction 10 Step 41 14.9683
Normal Mode Local Search Minimum 1275
Search Direction 1 Step 12 25.5916
Search Direction 2 Step 24 14.2499
Search Direction 3 Step 15 20.1340
Search Direction 4 Step 17 22.5360
Search Direction 5 Step 18 15.2485
Search Direction 6 Step 23 15.7879
Search Direction 7 Step 17 15.2485
Search Direction 8 Step 16 21.6798
Search Direction 9 Step 38 16.7975
Search Direction 10 Step 37 14.4265
Normal Mode Local Search Minimum 1276
Search Direction 1 Step 8 20.7474
Search Direction 2 Step 6 13.8502
Search Direction 3 Step 8 23.6899
Search Direction 4 Step 13 19.1020
Search Direction 5 Step 22 15.4630
Search Direction 6 Step 19 15.7042
Search Direction 7 Step 23 18.7117
Search Direction 8 Step 15 20.3688
Search Direction 9 Step 37 21.6078
Search Direction 10 Step 37 14.1897
whe280
commented
3 years ago Hello, thank you for your reply, I used the AT3_.sdf and command line you provided.It seems that Tinker failed when it first started running, and we are trying to find the error related to Tinker. The result is：
Running Tinker...
/home/node0/work/whe/tinker//bin/scan AT3_1 0 10 20 0.00001 | tee ./AT3_1.tout
Tinker job 1 of 2 completed.
/home/node0/work/whe/tinker//bin/scan AT3_2 0 10 20 0.00001 | tee ./AT3_2.tout
Tinker job 2 of 2 completed.
AT3_1 is matching conformational search output for AT3_1
Reading AT3_1
Traceback (most recent call last):
File "PyDP4.py", line 719, in <module>
main(settings)
File "PyDP4.py", line 212, in main
Isomers = Tinker.ReadConformers(TinkerOutputs, Isomers, settings)
File "/home/node0/work/whe/DP4-AI-master/Tinker.py", line 118, in ReadConformers
atoms, conformers, charge, AbsEs = ReadTinker(outp, settings, atypes, anums)
File "/home/node0/work/whe/DP4-AI-master/Tinker.py", line 155, in ReadTinker
MinE = min(energies)
ValueError: min() arg is an empty sequence
And here is the last 50 lines of AT3_1.sdf：
(my-rdkit-env) [node0@zhang8 DP4-AI-master]$ tail -50 AT3_1.tout
Additional Partial Charges for Specific Atoms :
Atom Charge
1 0.1900
2 -0.1500
3 -0.1500
4 -0.1500
5 0.1900
6 -0.1435
7 -0.1900
8 -0.1900
9 0.4135
10 -0.9000
11 0.2700
12 0.0000
13 0.0000
14 0.0000
15 0.0000
16 0.2800
17 -0.6800
18 0.1500
19 0.1500
20 0.1500
21 0.0000
22 0.0000
23 0.3600
24 0.0000
25 0.0000
26 0.0000
27 0.0000
28 0.0000
29 0.0000
30 0.0000
31 0.0000
32 0.0000
33 0.0000
34 0.0000
35 0.0000
36 0.4000
Number of Torsions Used in Derivative Computation : 9
Generating Seed Point for Potential Energy Surface Scan
GRADIENT -- Illegal Value for the Total Potential Energy
Tinker is Unable to Continue; Terminating the Current CalculationThanks a lot!I have tried looking at the starting sdf and the resulting sdf with Avogadro and not found the differences. The command I used was: python3 PyDP4.py -s chloroform -w mns -m t -f mmff AT3_1r.sdf AT3_2r.sdf NMR_folder It seems that Tinker failed when it first started running, and we are trying to find the error related to Tinker.
Here is the last 50 lines of AT3_1r.tout： (my-rdkit-env) [node0@zhang8 DP4-AI-master]$ tail -50 AT3_1r.tout
Additional Partial Charges for Specific Atoms :
Atom Charge
1 -0.1900
2 0.1900
3 -0.1500
4 -0.1500
5 -0.1500
6 0.1900
7 -0.1435
8 0.4135
9 -0.9000
10 0.2700
11 0.0000
12 0.2800
13 -0.6800
14 0.4000
15 0.1500
16 0.1500
17 0.1500
18 -0.1900
19 0.0000
20 0.0000
21 0.3600
22 0.0000
23 0.0000
24 0.0000
25 0.0000
26 0.0000
27 0.0000
28 0.0000
29 0.0000
30 0.0000
31 0.0000
32 0.0000
33 0.0000
34 0.0000
35 0.0000
36 0.0000Number of Torsions Used in Derivative Computation : 9
Generating Seed Point for Potential Energy Surface Scan
GRADIENT -- Illegal Value for the Total Potential Energy
Tinker is Unable to Continue; Terminating the Current Calculation
On 1/7/2021 22:08，KristapsEnotifications@github.com wrote：
Have you tried looking at the starting sdf and the resulting sdf with Avogadro or jmol or similar? The differences, if any, might provide clues as to what is going wrong.
You could also try skipping the diastereomer generation for now. Just renumber the AT3_1.sdf, AT3_2.sdf etc, and then submit them to PyDP4.py using python3 PyDP4.py -s chloroform -w mns -m t -f mmff AT3_1r.sdf AT3_2r.sdf NMR_folder
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KristapsE
commented
3 years ago Frankly, I am out of ideas, and ultimately I'm afraid it is an issue with TINKER, and not with DP4-AI. TINKER is not producing any conformers, so DP4-AI cannot generate any Gaussian input files. I can only suggest that you try contacting TINKER developers, but from my experience they are not too responsive. One last idea - could you perhaps try the precompiled binaries, instead of your compiled-from-source version, as others seem to have more luck with running the TINKER workflow?
whe280
commented
3 years ago Thank you for your patience to provide me with so many valuable suggestions these days. I will actively adopt your suggestions to update glibc to try to use the precompiled binaries, and try to find the problem with Tinker.Thanks and respect to you again. On 1/8/2021 23:20，KristapsEnotifications@github.com wrote：
Frankly, I am out of ideas, and ultimately I'm afraid it is an issue with TINKER, and not with DP4-AI. TINKER is not producing any conformers, so DP4-AI cannot generate any Gaussian input files. I can only suggest that you try contacting TINKER developers, but from my experience they are not too responsive. One last idea - could you perhaps try the precompiled binaries, instead of your compiled-from-source version, as others seem to have more luck with running the TINKER workflow?
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whe280
commented
3 years ago Hi,I have good news to share with you that the problem has been solved. PyDP4 process completed successfully after trying the precompiled binaries.Thanks a lot！ I ran Tinker Testing Outside the Script and found that Tinker failed to run (although the compilation process was fine,and it doesn't matter).
On 1/8/2021 23:20，KristapsEnotifications@github.com wrote：
Frankly, I am out of ideas, and ultimately I'm afraid it is an issue with TINKER, and not with DP4-AI. TINKER is not producing any conformers, so DP4-AI cannot generate any Gaussian input files. I can only suggest that you try contacting TINKER developers, but from my experience they are not too responsive. One last idea - could you perhaps try the precompiled binaries, instead of your compiled-from-source version, as others seem to have more luck with running the TINKER workflow?
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.
KristapsE
commented
3 years ago That's great to hear! I guess recommendation to use precompiled TINKER is something to add to the documentation.
@KristapsE hello，I am very interested in your research. There was an error while running this software. I have installed Tinker and G16, and I sincerely hope to get your help and advice. My command line is ‘python3 PyDP4.py -s chloroform -w gmns -m t -f mmff KE.sdf NMR_folder’.
========================== PyDP4 script, integrating Tinker/MacroModel, Gaussian/NWChem and DP4 v1.0
Copyright (c) 2015-2019 Kristaps Ermanis, Alexander Howarth, Jonathan M. Goodman Distributed under MIT license
Settings read from settings.cfg: SCHRODINGER: TinkerPath: /home/node0/work/whe/tinker NWChemPath: nwchem GausPath: g16 ['KE.sdf'] NMR_folder NMR_path /home/node0/work/whe/DP4-AI-master/NMR_folder Current working directory: /home/node0/work/whe/DP4-AI-master Initial input files: ['KE.sdf'] NMR file: [PosixPath('/home/node0/work/whe/DP4-AI-master/NMR_folder/Carbon'), PosixPath('/home/node0/work/whe/DP4-AI-master/NMR_folder/Proton')] Workflow: gmns
Generating diastereomers... Getting inchi from file KE.sdf Getting inchi from file KE.sdf Number of diastereomers to be generated: 2 Isomer 0 inchi = InChI=1S/C6H10O/c1-5-3-2-4-6(5)7/h2-3,5-7H,4H2,1H3/t5-,6-/m0/s1/f/ Isomer 1 inchi = InChI=1S/C6H10O/c1-5-3-2-4-6(5)7/h2-3,5-7H,4H2,1H3/t5-,6+/m0/s1/f/ Generated input files: ['KE1', 'KE2']
Assuming all computations are done? ... False Using preexisting DFT data? ... False Performing conformational search using Tinker
Setting up Tinker files... Tinker input for KE1 prepared. Tinker input for KE2 prepared.
Running Tinker... /home/node0/work/whe/tinker/bin/scan KE1 0 10 20 0.00001 | tee ./KE1.tout mmff.prm
Tinker job 1 of 2 completed. /home/node0/work/whe/tinker/bin/scan KE2 0 10 20 0.00001 | tee ./KE2.tout mmff.prm
Tinker job 2 of 2 completed. KE1 is matching conformational search output for KE1 Reading KE1 Tinker output KE1 is corrupted, aborting.