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starwingc / peptoid_24summer

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Problem with prepared three residues #2

Closed starwingc closed 4 months ago

starwingc commented 4 months ago

Hi @vvoelz , I am unable to prepared these three residues:

NMA, NXA, NXB under the residues/GAFF/modified/ all the file are created and checked, can you have a looks at them?

vvoelz commented 4 months ago

Sure -- I'll take a look! Which script breaks down, and at what point? Is there an error message?

starwingc commented 4 months ago

simply the build_amber_residue.py, I don't have the error message right now, but it is index out of list. While all other residues are run fine!

vvoelz commented 4 months ago

Hi @starwingc -- all of those residues have quatenary amines, and should be positive charged. There's a flag in the build_amber_residue.py script the specify the net charges (See: residues/GAFF/modified/NMA/runme_vav e.g.). I built the residues and pushed the results.

starwingc commented 4 months ago

[heart] Starwing Chen reacted to your message:

From: Vincent Voelz @.> Sent: Thursday, May 23, 2024 3:13:03 PM To: starwingc/peptoid_24summer @.> Cc: Starwing Chen @.>; Mention @.> Subject: [External] Re: [starwingc/peptoid_24summer] Problem with prepared three residues (Issue #2)

Hi @starwingchttps://github.com/starwingc -- all of those residues have quatenary amines, and should be positive charged. There's a flag in the build_amber_residue.py script the specify the net charges (See: residues/GAFF/modified/NMA/runme_vav e.g.). I built the residues and pushed the results.

— Reply to this email directly, view it on GitHubhttps://github.com/starwingc/peptoid_24summer/issues/2#issuecomment-2127391645, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BEMRYMVQD3GR4TRVQVBPGXTZDYBP7AVCNFSM6AAAAABIFXOQNWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRXGM4TCNRUGU. You are receiving this because you were mentioned.Message ID: @.***>

starwingc commented 4 months ago

[like] Starwing Chen reacted to your message:

From: Vincent Voelz @.> Sent: Thursday, May 23, 2024 3:13:03 PM To: starwingc/peptoid_24summer @.> Cc: Starwing Chen @.>; Mention @.> Subject: [External] Re: [starwingc/peptoid_24summer] Problem with prepared three residues (Issue #2)

Hi @starwingchttps://github.com/starwingc -- all of those residues have quatenary amines, and should be positive charged. There's a flag in the build_amber_residue.py script the specify the net charges (See: residues/GAFF/modified/NMA/runme_vav e.g.). I built the residues and pushed the results.

— Reply to this email directly, view it on GitHubhttps://github.com/starwingc/peptoid_24summer/issues/2#issuecomment-2127391645, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BEMRYMVQD3GR4TRVQVBPGXTZDYBP7AVCNFSM6AAAAABIFXOQNWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRXGM4TCNRUGU. You are receiving this because you were mentioned.Message ID: @.***>