Dear developers, Hello, I'm having some trouble using AutoMapper. 1. If you use the clean tooltip list index out of range, but the corresponding files are still generated, whether these files can be used? 2. The message "Missing Atom Search timed out" is displayed when map is generated using the file in Step 1. 3. How can these two problems be solved I am looking forward to your answer and wish you success in your work!

[yyc-525]

[yyc-525]

I tried several times, but still failed to solve these two problems. These are the files before and after the reaction and the files after clean that I created with moltemplate. If you have time, I hope you can help me check them. Thanks again for contributing to the fix/react template.

[m-bone]

Hi I'm afraid the files are aren't attached so I can't be of much help debugging them.

The error from the clean command means it hasn't worked and the files it releases are it's best attempt, to help you try and figure out why it's not worked. That is most likely why the map has failed.

Matt

[yyc-525]

Dear Matt
I have solved the problem of clean because there are too many unused parameters in the oplsaa force field, which is beyond the scope of the program. When I use the gaff force field, the problem does not arise.However, in the subsequent steps, the map has not been successfully generated. The command I used is python3 AutoMapper.py. map cleanedpre_ reaction.data cleanedpost_ reaction.data --save_ Name pre-molecule.data post-molecule.data -- ba 23 52 20 39 23 52 20 39 -- ebt C C C H H F N O. I will upload the data file and setting file after the gap force field is cleaned. Please check them for me. Wish you a happy life!
Young

[yyc-525]

Dear  Matt This is my relevant document. I look forward to your reply. Young

…

------------------ 原始邮件 ------------------ 发件人: "m-bone/AutoMapper" ***@***.***>; 发送时间: 2023年1月6日(星期五) 晚上10:59 ***@***.***>; 抄送: " 杨帅 ***@***.***>;"State ***@***.***>; 主题: Re: [m-bone/AutoMapper] Dear developers, Hello, I'm having some trouble using AutoMapper.=0A1. If you use the clean tooltip list index out of range, but the corresponding files are still generated, whether these files can be used?=0A2. The message "Missing Atom Search timed out" is displayed when map is generated using the file in Step 1.=0A3. How can these two problems be solved I am looking forward to your answer and wish you success in your work! (Issue #7) Hi I'm afraid the files are aren't attached so I can't be of much help debugging them. The error from the clean command means it hasn't worked and the files it releases are it's best attempt, to help you try and figure out why it's not worked. That is most likely why the map has failed. Matt — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you modified the open/close state.Message ID: ***@***.***>