search

Isra3l / ligpargen

MIT License
54 stars 20 forks source link

A error happened when running ligpargen #8

Closed TerryHangLyu closed 2 years ago

TerryHangLyu commented 2 years ago

Dear developer,

I installed ligpargen as suggested in the README.md. And when I ran the test, it seemed ok. But when I typed the command "ligpargen -s 'c1ccc(cc1)O'" in the terminal, a error happened, which said the file 'plt.pdb' doesn't exist. Now, the error also shows up even when I do not use the smiles string as input. I am writing to ask for help to get ligpargen installed correctly. Can you give me some advice to deal with it?

Best wishes, Hang LYU

PS: Test image The error image

TerryHangLyu commented 2 years ago

I have also tried to follow procedure suggested in the README.md to install ligpargen in different devices, but the same error sitll cannot be avoided.

Isra3l commented 2 years ago

Dear Hang,

Did you fix the error installing BOSS properly as I suggested to you in the email? (Probably 32 bits libraries missing)

Best,

Israel

TerryHangLyu commented 2 years ago

Dear Israel, Sorry for the late reply. Maybe something went wrong about my email, but I didn't receive the mail about the installation of BOSS from you. My email address is hlyuai@connect.ust.hk. Could you please resend to me the mail about installing BOSS? So sorry for bothering you again.

Best, Hang

TerryHangLyu commented 2 years ago

Dear Israel, Sorry for my late reply, I was really busy recently. I did install two 32 bits libraries (ld-linux.so.2 and libgcc_s.so.1) for BOSS, and BOSS can work now.

image

But when I tried the command "ligpargen -s 'c1ccc(cc1)O'". I still got the error report.

image

Best wishes, Hang LYU

TerryHangLyu commented 2 years ago

Dear Israel, Sorry for my late reply, I was really busy recently. I did install two 32 bits libraries (ld-linux.so.2 and libgcc_s.so.1) for BOSS, and BOSS can work now.

image

But when I tried the command "ligpargen -s 'c1ccc(cc1)O'". I still got the error report.

image

Best wishes, Hang LYU

I really don't know how to fix it. Can you give me some suggestions?

Isra3l commented 2 years ago

Dear Hang,

Have you tried the charge model CM1A? My version works fine and I suspect that the problem is your BOSS version. Probably you are using BOSS4.9 but you should use BOSS5.0 for the CM1A-LBCC charge model. Try:

ligpargen -s 'c1ccc(cc1)O -cgen CM1A -p mymol

If you have any errors, I would suggest you send an email to Bill Jorgensen and ask him to get the BOSS5.0 version. Just, tell him that you are interested in using the Ligpargen command-line version with CM1A-LBCC from my Github and you need BOSS5.0.

I hope it works,

Best,

Israel

TerryHangLyu commented 2 years ago

Dear Hang,

Have you tried the charge model CM1A? My version works fine and I suspect that the problem is your BOSS version. Probably you are using BOSS4.9 but you should use BOSS5.0 for the CM1A-LBCC charge model. Try:

ligpargen -s 'c1ccc(cc1)O -cgen CM1A -p mymol

If you have any errors, I would suggest you send an email to Bill Jorgensen and ask him to get the BOSS5.0 version. Just, tell him that you are interested in using the Ligpargen command-line version with CM1A-LBCC from my Github and you need BOSS5.0.

I hope it works,

Best,

Israel

Thanks so much for your suggestions! Will try it soon.

TerryHangLyu commented 2 years ago

Dear Israel,

Thanks for your help. I have contacted the developer of BOSS5.0 for the link to download it. After installing BOSS5.0, Ligpargen can work well in my computer now.

Best wishes and thanks, Hang LYU