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1

I have some questions to ask for clarification on my CYP3A4 MD modelling which has 2 Ligands (Z9Z and HEM) compared to HSP90 which has only one in the Template I am using.

Using both ligands amd only HEM for hydrated Ligands it gave me errors but when I use Z9Z to get my Hydrated Ligand no error was seen.

Is it right way to go using one Ligand to generate the Hydrated Ligand?
Thanks

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2

Hi Samuel, do you want to perform the modelling with both ligands or not?

Also, at which step do you see the error? With the acpype tool, or when merging the topologies?

All the best,

Simon

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Hi Simon thank you for the quick response

The error was seen at the merge topologies after the hydrated ligand gotten when I uses HEM or HEATM as match to get my Ligands PDB but do not encounter such error at Merge Topology when I use only Z9Z ligand to be use for my Ligand PDB.

On performing modelling on the two ligands I can"t say based on the fact that this is a new area to me but I think should be on the two but I need your opinion on this has an expert.

Thanks

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Could you share a link to your history please?

Regarding the ligands: it depends what exactly you are aiming to study about this protein. However, I think the heme group should definitely be modelled.

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Hi Simon,

I will.

Thank you.

Best regards,

6

Hi Simon,

The link was already shared.

Regards

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I’m really sorry for the slow reply, it seems I don’t get notified of messages on this forum for some reason.

Could you send me a link to the history? I couldn’t find it under the ‘Histories shared with me’ section.

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It would be best not to post those details on a public site like this.

Here is how to share a history:

  1. click on the wheel icon on the top right of the history

  2. click ‘Share or Publish’ in the dropdown menu

  3. tick ‘Also make all objects within the History accessible.’ (important!)

  4. click ‘make history accessible via link’

  5. you will see a URL, if you copy and send it to me I will be able to take a look

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10

Hi Simon,

I’m very sorry to be bordering you.

I have made my link visible a long time ago but I couldn’t get any response from the link using the share /publish from the history.

Here is my Link : https://usegalaxy.eu/u/samuel/h/copy-of-wild-type-cyp3a4
https://usegalaxy.eu/u/samuel/h/hsp90-structure

Thank you very much Simon .

Samuel

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It’s no bother at all!

Unfortunately I cannot see the datasets - you need to make sure to tick ‘Also make all objects within the History accessible.’ when you share the history.

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Hi Simon,

Thank you very much for your reply Simon.

KIndly put me through on which one is the appropriate via this snap chat.

Regards

Screenshot (62).png
Screenshot (62).png1366×768 128 KB

Screenshot (64).png
Screenshot (64).png1366×768 71.6 KB

Screenshot (63).png
Screenshot (63).png1366×768 133 KB

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Hi Samuel, the last screenshot looks correct to me. I can now see your Hsp90 history, but not the CYP one - I’m not sure why that is.

It looks like you are using old versions of the tools, can you use more recent ones at this link: https://usegalaxy.eu/?tool_id=gmx_sim? 2020.2+galaxy0 is the most recent version, which is also the one used in the Hsp90 tutorial.

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Btw, you can use that tool I linked for all NPT + NVT + production simulations - it’s described that way as well in the tutorial.

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Hi Simon,

I will also use the new link provided.

Thank you always.

Regards,
Samuel

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