Error while generating topologies

[91Abdullah]

Error while generating topologies

[lkagami]

Dear Acpype user,
Try to use Openbabel in your ligant before running ACPYPE. This process can update the atom names..
Thank you for use ACPYPE!
Regards,
Luciano

[91Abdullah]

Dear @lkagami ,

Thanks for providing help in the matter. However, I am using babel minimize before acpype for generating parameters. Did you specifically mean some other function?

Regards,
Abdullah

[alanwilter]

Dear Abdullah, In my experience, you're mixing up topology blocks of protein and ligand in the top file. There's a specific other and I believe the information about atom c6 (which I believe is in the itp file from ACPYPE), is not being picked up once you created the top file. The best place to get this sorted is GMX webmail list as this is not the first time this issue has been reported. Thanks for using ACPYPE. Alan

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On Mon, 25 Sept 2023 at 12:42, Syed Abdullah Basit ***@***.***> wrote: Dear @lkagami <https://github.com/lkagami> , Thanks for providing help in the matter. However, I am using babel minimize before acpype for generating parameters. Did you specifically mean some other function? Regards, Abdullah — Reply to this email directly, view it on GitHub <#104 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA5YDSRJV7IFYXT7J276N3DX4FU2RANCNFSM6AAAAAA5FYHFSA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Alan Silva 🚲🏊‍♂🏃‍♂🇧🇷🇫🇷🇬🇧