Dear Andre, I am not sure what you mean by conformational space around the model, but to answer your question: short energy minimization can be done using, for example, deep view/swiss pdb viewer. However, I think that you are most likely looking for a short bout of molecular dynamics, in which you can use explicit solvent and a proper ionic envelope. There you have a few options - GROMACS, NAMD, AMBER etc. The first 2 are free for academia, but if you have no prior knowledge of MD it can be a little bit tricky to set the system up correctly. Let me know if I can help further.
Best, Sorin On Wed, Jun 24, 2020 at 10:08 PM Andre LB Ambrosio <an...@ifsc.usp.br> wrote: > Dear colleagues, > > could you please suggest a computational tool to perform energy > minimization of a crystal structure under explicit solvent conditions (i.e, > types and concentrations of ions, pH)? > > I want to observe the solvent effects on the conformational space around a > starting model, all-atom, while preserving its geometry (I guess it can be > better expressed as relaxation). > > Thank you in advance. > > -- > Andre LB Ambrosio > > ------------------------------ > > 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/
