DeNovo problem #4

aluisiomf · 2021-12-06T12:44:42Z

Dear
I'm Prof. Aluisio, from UNILAB, Brazil. I am delighted with the results obtained by you through MolAICal. I started training the Denovo method and followed all the steps in the tutorial. But the only answer I got was this one, which is just below. How should I proceed?
I await your return.
Greetings.

https://drive.google.com/file/d/1GBnBcyTsE3lEz80_JwBIYrElg6zdcZQX/view?usp=sharing

MolAICal · 2021-12-06T14:43:26Z

Dear I'm Prof. Aluisio, from UNILAB, Brazil. I am delighted with the results obtained by you through MolAICal. I started training the Denovo method and followed all the steps in the tutorial. But the only answer I got was this one, which is just below. How should I proceed? I await your return. Greetings.

https://drive.google.com/file/d/1GBnBcyTsE3lEz80_JwBIYrElg6zdcZQX/view?usp=sharing

Dear Prof. Aluisio,

I think it is the path string problem. System cannot recognize string "program%20File" (please see below figure). Could you please put the MolAICal into D: disk root rather than into c:\program%20File? For example, install MolAICal into d:\MolAICal-win64, and set the environment, and then run the command as shown in your figure.

Of course, you can install MolAICal into any directory that is without special characters.

If you have any problem, please add the issue to tell me.

Best,
Qifeng

aluisiomf · 2021-12-06T15:00:59Z

Dear Thank you very much for the instruction. It's working now. I hope the procedure is over. Greetings. Em seg., 6 de dez. de 2021 às 11:43, MolAICal ***@***.***> escreveu:

…

Dear I'm Prof. Aluisio, from UNILAB, Brazil. I am delighted with the results obtained by you through MolAICal. I started training the Denovo method and followed all the steps in the tutorial. But the only answer I got was this one, which is just below. How should I proceed? I await your return. Greetings. https://drive.google.com/file/d/1GBnBcyTsE3lEz80_JwBIYrElg6zdcZQX/view?usp=sharing Dear Prof. Aluisio, I think it is the path string problem. System cannot recognize string "program%20File" (please see below figure). Could you please put the MolAICal into D: disk root rather than into c:\program%20File? For example, install MolAICal into d:\MolAICal-win64, and set the environment, and then run the command as shown in your figure. If you have any problem, please add the issue to tell me. [image: f1] <https://user-images.githubusercontent.com/34206645/144866000-100f41eb-39c7-4a44-898e-591e163ba11c.png> Best, Qifeng — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AWZSJYN6ZJ3EBOHONT2UOF3UPTDZRANCNFSM5JOQ72EQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- *Prof. Dr. Aluísio Marques da Fonseca* *University of International Integration of Afro-Brazilian Lusophony (UNILAB) * *Institute of Exact and Nature Sciences (ICEN)* *Academic Master's degree in Sociobiodiversity and Sustainable Technologies (MASTS)* *Tels: (85) 98811-2586/ (85) 99635-4595* Interdisciplinary Group in Chemistry (GIQ) https://orcid.org/0000-0002-8112-9513 http://www.researcherid.com/rid/G-7002-2015 http://lattes.cnpq.br/5317597427402651 *http://www.wix.com/aluisiomf/teste-etnobotanicoshttp://www.wix.com/aluisiomf/emol <http://www.wix.com/aluisiomf/emol>* *http://www.wix.com/aluisiomf/biocatalise <http://www.wix.com/aluisiomf/biocatalise>*

aluisiomf · 2021-12-11T10:59:26Z

Expensive
Now I have a new problem.
When I leave processing through the command prompt this message appears:
Figure 1.
https://drive.google.com/file/d/1V5lIpHYdFnErt8_oLltrxZjxeQD1hnlv/view?usp=sharing

I left for 48h and so far nothing appeared in the folder "results"
Figure 2.
https://drive.google.com/file/d/1CzZohCT7JGq-qa27GIEiSd93smV-xgI5/view?usp=sharing

Is the problem related to the path of the Babel gui? Here is the file (InputParFileAI.dat).
Figure 3.
https://drive.google.com/file/d/16A4RdrB5kXpSSen7pqHmpvAXw6QoWjNQ/view?usp=sharing

Archive 1
https://drive.google.com/file/d/1MYPy7yWu3RdPFD8TRUlTOXorBFl8untC/view?usp=sharing

I'm waiting for your answer.
Greetings.

MolAICal · 2021-12-13T13:57:49Z

Expensive Now I have a new problem. When I leave processing through the command prompt this message appears: Figure 1. https://drive.google.com/file/d/1V5lIpHYdFnErt8_oLltrxZjxeQD1hnlv/view?usp=sharing

I left for 48h and so far nothing appeared in the folder "results" Figure 2. https://drive.google.com/file/d/1CzZohCT7JGq-qa27GIEiSd93smV-xgI5/view?usp=sharing

Is the problem related to the path of the Babel gui? Here is the file (InputParFileAI.dat). Figure 3. https://drive.google.com/file/d/16A4RdrB5kXpSSen7pqHmpvAXw6QoWjNQ/view?usp=sharing

Archive 1 https://drive.google.com/file/d/1MYPy7yWu3RdPFD8TRUlTOXorBFl8untC/view?usp=sharing

I'm waiting for your answer. Greetings.

Dear prof. Aluisio,

It seems your computer does not run fast, you can employ the multicore server to run it. obabelPath parameter has been deprecated (see MolAICal v1.1 manual). If you want to show results, you can reduce computing cost by modifying parameters in file "InputParFileAI.dat" as follows:

numCycleGen             	6
randomCrossMutation       off
selBindingScore			0
perturbeSearch              off

The detail information about above parameters can be found in MolAICal manual.

Best,
Qifeng

aluisiomf · 2021-12-13T16:02:00Z

Dear,
Very grateful for the answers.
I'm in another problem.
When I run the InputParFileAI file.dat and add those modifications suggested by you, I can generate the 120 fragments in the tmpGenMols folder. However, as soon as they are the procedure close suddenly with the following message shown in figure 1.

Figure 1. https://drive.google.com/file/d/1HFPB18QBttQ0uoCHxGYhdlgxyrP8m1rw/view?usp=sharing

How should I proceed now?
I await your return.

MolAICal · 2021-12-13T16:09:40Z

Dear, Very grateful for the answers. I'm in another problem. When I run the InputParFileAI file.dat and add those modifications suggested by you, I can generate the 120 fragments in the tmpGenMols folder. However, as soon as they are the procedure close suddenly with the following message shown in figure 1.

Figure 1. https://drive.google.com/file/d/1HFPB18QBttQ0uoCHxGYhdlgxyrP8m1rw/view?usp=sharing

How should I proceed now? I await your return.

It seems previous problem. Could you delete folder "tmpGenMols", and run command in your figure again? If you have any problem, please feed it back to me.

aluisiomf · 2021-12-13T20:40:27Z

Dear,
After the command, continued with the same message, as shown in Figure 1. Where it references a change in the "-45,011000". Besides, it's not generating the results. What does that mean? I did the whole manual procedure. I would love to use this method for the development of my research.

https://drive.google.com/file/d/1EaGPDM7619CE-t8kYNakdv7UeXAqN3We/view?usp=sharing

I await your return.
Greetings.

MolAICal · 2021-12-14T08:41:56Z

Dear prof. Aluisio,

Dear prof. Aluisio,

It seems your windows DOS does not use english UTF-8 default, please input command and press enter key like below figure: chcp 65001

and run command above your supplied figure.
if you have any problem, please give me message.

Best,
Qifeng

MolAICal · 2021-12-14T11:18:03Z

Dear, After the command, continued with the same message, as shown in Figure 1. Where it references a change in the "-45,011000". Besides, it's not generating the results. What does that mean? I did the whole manual procedure. I would love to use this method for the development of my research.

https://drive.google.com/file/d/1EaGPDM7619CE-t8kYNakdv7UeXAqN3We/view?usp=sharing

I await your return. Greetings.

Dear prof. Aluisio,

Is it OK when you use command: chcp 65001, and follow, run molaical for de novo drug design?

If not, please use: chcp 936 or chcp 437, and then, try to input command for molecular growth. My DOS console is 936.

Please feed message back to me whether it is OK.

Thanks,

Qifeng

aluisiomf · 2021-12-15T16:20:58Z

Dear,
I believe there's been a breakthrough. But it didn't reach the end of the process. I just gave up doing it for MS DOS and used Power Shell. The process was up to the 30cycle. However when he informed that it would generate the output the system closed with the following message:

Exception in thread "main" java.lang.NumberFormatException: For input string: "0.150981".
https://drive.google.com/file/d/14zGdTnk3QmeSOZEoXLR3rX3Py9HAdNpU/view?usp=sharing

The process lasted approximately 6 hours.
The file was generated: tmpLigands.mol2. This file presented 2060 binders.
https://drive.google.com/file/d/11iY1JoWWKMqzrU4DfIO-QjnwqikJJ951/view?usp=sharing

I really need more information. I believe there's not much left to actually use this method of drug design.
I used this file .dat to process:
https://drive.google.com/file/d/1vebugWFqxgXx2SPNz_QhGmObU2Z6UkDE/view?usp=sharing

MolAICal · 2021-12-15T17:26:47Z

Dear, I believe there's been a breakthrough. But it didn't reach the end of the process. I just gave up doing it for MS DOS and used Power Shell. The process was up to the 30cycle. However when he informed that it would generate the output the system closed with the following message:

Exception in thread "main" java.lang.NumberFormatException: For input string: "0.150981". https://drive.google.com/file/d/14zGdTnk3QmeSOZEoXLR3rX3Py9HAdNpU/view?usp=sharing

The process lasted approximately 6 hours. The file was generated: tmpLigands.mol2. This file presented 2060 binders. https://drive.google.com/file/d/11iY1JoWWKMqzrU4DfIO-QjnwqikJJ951/view?usp=sharing

I really need more information. I believe there's not much left to actually use this method of drug design. I used this file .dat to process: https://drive.google.com/file/d/1vebugWFqxgXx2SPNz_QhGmObU2Z6UkDE/view?usp=sharing

First of all, could you compress all files in your 000-AIGrow and share it to me? I help you check it.

Secondly, could you activiate command chcp 936 in your power shell? if yes, please use it, and then, input command for molecular growth. Please set 5 cycle for testing because it can fastly get results.

MolAICal · 2021-12-16T07:11:57Z

Dear, I believe there's been a breakthrough. But it didn't reach the end of the process. I just gave up doing it for MS DOS and used Power Shell. The process was up to the 30cycle. However when he informed that it would generate the output the system closed with the following message:

Dear prof. Aluisio,

I think encoding is the main reason for this bug. Windows use different default encodings in different countries. Molecular growth part of MolAICal is developed based on UTF-8 encoding. So please change your character set to UTF-8. For more detail encoding character set information, please check: https://developpaper.com/question/how-to-make-the-windows-command-line-support-utf-8-character-set/

Please follow my instruction, so I can find the problem, input below command in MS-DOS or powershell and press "Enter" key in your keyboard:

chcp 65001

At last, input MolAICal command for molecular grow.

Best,
Qifeng

aluisiomf · 2021-12-16T17:57:27Z

Dear Qifeng,
I switched to HTF-8, via chcp 65001.
As shown in fig.1.
https://drive.google.com/file/d/1m9Doa8g5zeHhlJM5jPYzvKyKXzMGJ5cs/view?usp=sharing

The end result is always the same as the previous ones.

The file folder I obtained is attached.
https://drive.google.com/file/d/1DAicaz-bCr7LzVzLBVT3y31Msnh4__ZC/view?usp=sharing

Please see if the problem may be related to the output of the file: InputParFileAI.dat.
I'm waiting for a return.
Greetings

MolAICal · 2021-12-17T12:56:00Z

Dear Qifeng, I switched to HTF-8, via chcp 65001. As shown in fig.1. https://drive.google.com/file/d/1m9Doa8g5zeHhlJM5jPYzvKyKXzMGJ5cs/view?usp=sharing

The end result is always the same as the previous ones.

The file folder I obtained is attached. https://drive.google.com/file/d/1DAicaz-bCr7LzVzLBVT3y31Msnh4__ZC/view?usp=sharing

Please see if the problem may be related to the output of the file: InputParFileAI.dat. I'm waiting for a return. Greetings

Dear prof. Aluisio,

Thanks for your report. It is the bug of MolAICal. I forgot different countries have different language styles. I have fix the problem, please download the development version of MolAICal as follows:

click and download MolAICal:

In addition, you can also download the development version of MolAICal from google drive: https://drive.google.com/file/d/1DbXYdOVaAOo-RxhWZq_1ivXkhSamSh2-/view?usp=sharing

Please use development version of MolAICal to repeat above molecular growth, and feed back the final results to me whether it succeeds or fails.

Best,
Qifeng

MolAICal · 2021-12-17T16:39:32Z

Dear Qifeng, I switched to HTF-8, via chcp 65001. As shown in fig.1. https://drive.google.com/file/d/1m9Doa8g5zeHhlJM5jPYzvKyKXzMGJ5cs/view?usp=sharing

Besides, please delete file tmpLigands.mol2 and remove folder tmpGen before running above molecular grow, because they have contained weird characters.

aluisiomf · 2021-12-18T10:49:49Z

Dear Qifeng,
I'm not getting to download this folder. Always ends halfway through the download, 1.31Gb.
Would there be any other links or are you having folder release issues?
I'll wait for a solution.

MolAICal · 2021-12-18T11:39:33Z

Dear Qifeng, I'm not getting to download this folder. Always ends halfway through the download, 1.31Gb. Would there be any other links or are you having folder release issues? I'll wait for a solution.

What about google Drive: https://drive.google.com/file/d/1DbXYdOVaAOo-RxhWZq_1ivXkhSamSh2-/view?usp=sharing

In addition, I supply 6 routes for downloading in MolAICal web. Which route is fast for you. I can upload MolAICal into it for your download.

aluisiomf · 2021-12-18T13:08:50Z

Dear,
I want to express my happiness to see that the results were obtained in molecular growth.
The problem was in the previous folder.
Thank you very much, and soon I will be consulting you for further questions.
Let's follow the study of computer simulations.
Greetings.

MolAICal · 2021-12-18T13:49:24Z

Dear, I want to express my happiness to see that the results were obtained in molecular growth. The problem was in the previous folder. Thank you very much, and soon I will be consulting you for further questions. Let's follow the study of computer simulations. Greetings.

Greatly! By the way, which version of MolAICal is used for you at this time: v1.1 or development version?

aluisiomf · 2021-12-18T15:23:09Z

I used this link you suggested to download:
What about google Drive: https://drive.google.com/file/d/1DbXYdOVaAOo-RxhWZq_1ivXkhSamSh2-/view?usp=sharing

nyy777 · 2022-03-13T02:37:30Z

亲爱的，我是来自巴西UNILAB的Aluisio教授。我对您通过MolAICal获得的结果感到高兴。我开始训练Denovo方法，并按照教程中的所有步骤进行操作。但我得到的唯一答案是这个，就在下面。我应该如何操作？我等待你的回来。问候。

https://drive.google.com/file/d/1GBnBcyTsE3lEz80_JwBIYrElg6zdcZQX/view?usp=sharing

您好！没有特殊字符串也会有这个错误是为什么呢？希望得到您的解答，谢谢！

MolAICal · 2022-03-13T07:04:17Z

亲爱的，我是来自巴西UNILAB的Aluisio教授。我对您通过MolAICal获得的结果感到高兴。我开始训练Denovo方法，并按照教程中的所有步骤进行操作。但我得到的唯一答案是这个，就在下面。我应该如何操作？我等待你的回来。问候。
https://drive.google.com/file/d/1GBnBcyTsE3lEz80_JwBIYrElg6zdcZQX/view?usp=sharing

您好！没有特殊字符串也会有这个错误是为什么呢？希望得到您的解答，谢谢！

Thanks for your attention. If you use Chinese words, please paste your problems in https://github.com/MolAICal/documents/issues or https://github.com/MolAICal/documents/issues

including the version of MolAICal you used, and screenshot for meeting problem.

Thanks,
Qifeng

nyy777 · 2022-03-14T01:53:30Z

亲爱的，我是来自巴西UNILAB的Aluisio教授。我对您通过MolAICal获得的结果感到高兴。我开始训练Denovo方法，并按照教程中的所有步骤进行操作。但我得到的唯一答案是这个，就在下面。我应该如何操作？我等待你的回来。问候。
https://drive.google.com/file/d/1GBnBcyTsE3lEz80_JwBIYrElg6zdcZQX/view?usp=sharing

您好！没有特殊字符串也会有这个错误是为什么呢？希望得到您的解答，谢谢！

Thanks for your attention. If you use Chinese words, please paste your problems in https://github.com/MolAICal/documents/issues or https://github.com/MolAICal/documents/issues

including the version of MolAICal you used, and screenshot for meeting problem.

Thanks, Qifeng

Hello! There will be this error without a special string. Why? Hope to get your answer, thank you!

MolAICal · 2022-03-16T06:20:35Z

亲爱的，我是来自巴西UNILAB的Aluisio教授。我对您通过MolAICal获得的结果感到高兴。我开始训练Denovo方法，并按照教程中的所有步骤进行操作。但我得到的唯一答案是这个，就在下面。我应该如何操作？我等待你的回来。问候。
https://drive.google.com/file/d/1GBnBcyTsE3lEz80_JwBIYrElg6zdcZQX/view?usp=sharing

您好！没有特殊字符串也会有这个错误是为什么呢？希望得到您的解答，谢谢！

Thanks for your attention. If you use Chinese words, please paste your problems in https://github.com/MolAICal/documents/issues or https://github.com/MolAICal/documents/issues
including the version of MolAICal you used, and screenshot for meeting problem.
Thanks, Qifeng

Hello! There will be this error without a special string. Why? Hope to get your answer, thank you!

Could you answer below questions?

Do you install MolAICal v1.3 following the install instruction: https://molaical.github.io/install.html
Which version and type of linux do you use? For example, ubuntu x86_64, etc

MolAICal · 2022-03-16T06:23:54Z

亲爱的，我是来自巴西UNILAB的Aluisio教授。我对您通过MolAICal获得的结果感到高兴。我开始训练Denovo方法，并按照教程中的所有步骤进行操作。但我得到的唯一答案是这个，就在下面。我应该如何操作？我等待你的回来。问候。
https://drive.google.com/file/d/1GBnBcyTsE3lEz80_JwBIYrElg6zdcZQX/view?usp=sharing

您好！没有特殊字符串也会有这个错误是为什么呢？希望得到您的解答，谢谢！

Thanks for your attention. If you use Chinese words, please paste your problems in https://github.com/MolAICal/documents/issues or https://github.com/MolAICal/documents/issues
including the version of MolAICal you used, and screenshot for meeting problem.
Thanks, Qifeng

Hello! There will be this error without a special string. Why? Hope to get your answer, thank you!

Could you answer below questions?

Do you install MolAICal v1.3 following the install instruction: https://molaical.github.io/install.html
Which version and type of linux do you use? For example, ubuntu x86_64, etc

nyy777 · 2022-03-16T07:03:39Z

亲爱的，我是来自巴西UNILAB的Aluisio教授。我对您通过MolAICal获得的结果感到高兴。我开始训练Denovo方法，并按照教程中的所有步骤进行操作。但我得到的唯一答案是这个，就在下面。我应该如何操作？我等待你的回来。问候。
https://drive.google.com/file/d/1GBnBcyTsE3lEz80_JwBIYrElg6zdcZQX/view?usp=sharing

您好！没有特殊字符串也会有这个错误是为什么呢？希望得到您的解答，谢谢！

Thanks for your attention. If you use Chinese words, please paste your problems in https://github.com/MolAICal/documents/issues or https://github.com/MolAICal/documents/issues
including the version of MolAICal you used, and screenshot for meeting problem.
Thanks, Qifeng

Hello! There will be this error without a special string. Why? Hope to get your answer, thank you!

Could you answer below questions?

Do you install MolAICal v1.3 following the install instruction: https://molaical.github.io/install.html

Which version and type of linux do you use? For example, ubuntu x86_64, etc
Thanks for your answer! yes i have successfully installed
The Ubuntu version is as follows, I am wondering if the version is too high? Hope to get your answer again！
abb0e9ca1d8942c308e59f9a6e1e05b

nyy777 · 2022-03-16T07:05:13Z

Thanks for your answer! yes i have successfully installed
The Ubuntu version is as follows, I am wondering if the version is too high? Hope to get your answer again

MolAICal · 2022-03-16T10:05:49Z

Thanks for your answer! yes i have successfully installed The Ubuntu version is as follows, I am wondering if the version is too high? Hope to get your answer again

Please input below commands in linux console and paste the run screenshot to me:

source <your install path>/MolAICal-linux64/mtools/py/bin/activate
python <your install path>/MolAICal-linux64/mtools/organ/main.py -f tmp.dat -s FDAFrag -n 100

nyy777 · 2022-03-17T04:11:35Z

Thanks for your answer! yes i have successfully installed The Ubuntu version is as follows, I am wondering if the version is too high? Hope to get your answer again

Please input below commands in linux console and paste the run screenshot to me:

source <your install path>/MolAICal-linux64/mtools/py/bin/activate
python <your install path>/MolAICal-linux64/mtools/organ/main.py -f tmp.dat -s FDAFrag -n 100

MolAICal · 2022-03-17T05:03:01Z

Thanks for your answer! yes i have successfully installed The Ubuntu version is as follows, I am wondering if the version is too high? Hope to get your answer again

Please input below commands in linux console and paste the run screenshot to me:
source <your install path>/MolAICal-linux64/mtools/py3/bin/activate python <your install path>/MolAICal-linux64/mtools/organ/main.py -f tmp.dat -s FDAFrag -n 100

It indicates you can not install MolAICal correctly. Please install MolAICal following linux install part step by step. And give me the install screenshot, so I can find your install problem.

nyy777 · 2022-03-17T10:19:12Z

Thanks for your answer! yes i have successfully installed The Ubuntu version is as follows, I am wondering if the version is too high? Hope to get your answer again

Please input below commands in linux console and paste the run screenshot to me:
source <your install path>/MolAICal-linux64/mtools/py3/bin/activate python <your install path>/MolAICal-linux64/mtools/organ/main.py -f tmp.dat -s FDAFrag -n 100

It indicates you can not install MolAICal correctly. Please install MolAICal following linux install part step by step. And give me the install screenshot, so I can find your install problem.

I reinstalled it again. It's no problem now. Thank you so much！

MolAICal closed this as completed Mar 17, 2022

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aluisiomf commented Dec 18, 2021

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MolAICal commented Mar 17, 2022

nyy777 commented Mar 17, 2022

DeNovo problem #4

DeNovo problem #4

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