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 <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 Get Outlook for Android<https://aka.ms/ghei36> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
