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 <artem.evdoki...@gmail.com> Sent: Friday, June 16, 2023 5:40 PM To: Veerendra Kumar <vkuma...@amity.edu> 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 <vkuma...@amity.edu<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 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/
