Re: [ccp4bb] Adding metal ions

[Veerendra Kumar]

Dear Jose, 

I want to simulate the copper/protein complex to track the movement of copper 
ion from the surface to its binding site. 

Best 
Veerendra 

-Original Message-
From: CCP4 bulletin board  On Behalf Of Jose Brandao-Neto
Sent: Tuesday, June 20, 2023 11:23 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Adding metal ions

Dear Veerendra,

 out of curiosity, what is your goal in doing this model? to simulate a copper 
solution?

regards,
Jose'


===
Jose Brandao-Neto MPhil CPhys
Operational Excellence Champion
Senior Beamline Scientist - I04-1
XChem Scientist
Diamond Light Source

jose.brandao-n...@diamond.ac.uk
+44 (0)1235 778506
===



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Re: [ccp4bb] Adding metal ions

[Jose Brandao-Neto]

Dear Veerendra,

 out of curiosity, what is your goal in doing this model? to simulate a copper 
solution?

regards,
Jose'


===
Jose Brandao-Neto MPhil CPhys
Operational Excellence Champion
Senior Beamline Scientist - I04-1
XChem Scientist
Diamond Light Source

jose.brandao-n...@diamond.ac.uk
+44 (0)1235 778506
===



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Re: [ccp4bb] Adding metal ions

[Veerendra Kumar]

Dear All,
Thank you for your suggestions. I managed to add ions as Dr Artem suggested. I 
added water using Charmm-gui. Then selected water molecules with 5A from 
protein surface and deleted rest water. Then finally replaced water with copper 
ions.

Best Regards
Veerendra

From: Artem Evdokimov 
Sent: Friday, June 16, 2023 5:40 PM
To: Veerendra Kumar 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Adding metal ions

Take a protein structure with waters, replace surface waters with Cu++ and run 
some very basic MD to optimize distances. Many of the atoms will move since 
Cu++ will find itself in an 'unfriendly' environment, as always caveat emptor :)

Artem

- Cosmic Cats approve of this message


On Fri, Jun 16, 2023 at 12:00 AM Veerendra Kumar 
mailto:vkuma...@amity.edu>> wrote:
Dear All,
I want to add about 200 copper ions on protein surface randomly. Is there any 
program available to serve the purpose?

Thank you
Best regards
Veerendra

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Re: [ccp4bb] Adding metal ions

[Artem Evdokimov]

Take a protein structure with waters, replace surface waters with Cu++ and
run some very basic MD to optimize distances. Many of the atoms will move
since Cu++ will find itself in an 'unfriendly' environment, as always
caveat emptor :)

Artem

- Cosmic Cats approve of this message


On Fri, Jun 16, 2023 at 12:00 AM Veerendra Kumar  wrote:

> Dear All,
> I want to add about 200 copper ions on protein surface randomly. Is there
> any program available to serve the purpose?
>
> Thank you
> Best regards
> Veerendra
>
> Get Outlook for Android 
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Adding metal ions

[Krieger, James M]

Charmm-gui can add copper ions and lots of other ones.

They seem to have removed the option of adding specific ions by numbers and 
instead give a box for concentration and an option to check how many there are. 
This depends a lot on the size of the box around the protein and you can maybe 
do a rough back of the envelope calculation to get started.

You would also need to set the padding distance to zero to get the ions on or 
near the protein surface. We tend to use around 10A either side for MD 
simulations to avoid the protein seeing itself across the periodic boundary, 
maybe even more padding if we expect significant conformational changes.

They also seem to only have an option of adding them in neutral pairs so you’d 
have to remove chloride ions afterwards.

Best wishes
James

On 16 Jun 2023, at 06:00, Veerendra Kumar  wrote:


Dear All,
I want to add about 200 copper ions on protein surface randomly. Is there any 
program available to serve the purpose?

Thank you
Best regards
Veerendra

Get Outlook for Android



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[ccp4bb] Adding metal ions

[Veerendra Kumar]

Dear All,
I want to add about 200 copper ions on protein surface randomly. Is there any 
program available to serve the purpose?

Thank you
Best regards
Veerendra

Get Outlook for Android



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