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maccallumlab / meld

Modeling with limited data
http://meldmd.org
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Suggestion : Add nucleotide forcefields to parser - OL3 for RNA and DNA.OL15 for DNA #148

Open yoavatsmonraz opened 1 year ago

yoavatsmonraz commented 1 year ago

It would be really useful for a wide variety systems of it was possible on an input level to parse nucleotides, would that be possible at all ? It seems like a small modification (relatively speaking)?

jlmaccal commented 1 year ago

I think it might be possible to do this already. You can build systems from pdb and can add in extra leap commands as part of the MELD setup.

As for building from sequence, that would certainly be possible. It would just require some additional code to support. I don't think that's something my group can committ to at this point, but if someone from the nucleotide community wants to do this, we would be happy to include it.

yoavatsmonraz commented 1 year ago

Thanks for the prompt response @jlmaccal , i recently read MELD DNA's paper which approached it by using psuedo atoms in their code, but I'm actually interested in directly importing an existing nucleotide-protein topology. I'll look into MELD's existing code to see how it can be modified via cpptraj.

jlmaccal commented 1 year ago

I would look at the Amber system builder classes. These are basically just a wrapper around tleap. We recently added support for the martini force field, so there might be some rough edges around the system builders. But it should be straightforward to add nucleic acid support.

From: yoavatsmonraz @.> Date: Thursday, May 18, 2023 at 4:01 PM To: maccallumlab/meld @.> Cc: Justin MacCallum @.>, Mention @.> Subject: Re: [maccallumlab/meld] Suggestion : Add nucleotide forcefields to parser - OL3 for RNA and DNA.OL15 for DNA (Issue #148)

Thanks for the prompt response @jlmaccalhttps://github.com/jlmaccal , i recently read MELD DNA's paper which approached it by using psuedo atoms in their code, but I'm actually interested in directly importing an existing nucleotide-protein topology. I'll look into MELD's existing code to see how it can be modified via cpptraj.

— Reply to this email directly, view it on GitHubhttps://github.com/maccallumlab/meld/issues/148#issuecomment-1553718092, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAA2MVYOAHDCF7S572BAJT3XG2LY5ANCNFSM6AAAAAAYARDRQI. You are receiving this because you were mentioned.Message ID: @.***>

alberto99 commented 1 year ago

Hi, We have used parmbsc1 for protein-DNA, and OL3 for RNA during the RNA puzzles competition. We used to have the ability to input a topology/coordinate pair as well – but have not used this in a while.

From: Justin MacCallum @.> Date: Thursday, May 18, 2023 at 8:16 PM To: maccallumlab/meld @.> Cc: Subscribed @.***> Subject: Re: [maccallumlab/meld] Suggestion : Add nucleotide forcefields to parser - OL3 for RNA and DNA.OL15 for DNA (Issue #148) I would look at the Amber system builder classes. These are basically just a wrapper around tleap. We recently added support for the martini force field, so there might be some rough edges around the system builders. But it should be straightforward to add nucleic acid support.

From: yoavatsmonraz @.> Date: Thursday, May 18, 2023 at 4:01 PM To: maccallumlab/meld @.> Cc: Justin MacCallum @.>, Mention @.> Subject: Re: [maccallumlab/meld] Suggestion : Add nucleotide forcefields to parser - OL3 for RNA and DNA.OL15 for DNA (Issue #148)

Thanks for the prompt response @jlmaccalhttps://github.com/jlmaccal , i recently read MELD DNA's paper which approached it by using psuedo atoms in their code, but I'm actually interested in directly importing an existing nucleotide-protein topology. I'll look into MELD's existing code to see how it can be modified via cpptraj.

— Reply to this email directly, view it on GitHubhttps://github.com/maccallumlab/meld/issues/148#issuecomment-1553718092, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAA2MVYOAHDCF7S572BAJT3XG2LY5ANCNFSM6AAAAAAYARDRQI. You are receiving this because you were mentioned.Message ID: @.***>

— Reply to this email directly, view it on GitHubhttps://github.com/maccallumlab/meld/issues/148#issuecomment-1553836714, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AABTLHAFUGS3UWQOLPFHIN3XG23XFANCNFSM6AAAAAAYARDRQI. You are receiving this because you are subscribed to this thread.Message ID: @.***>