Dear Sorin, many thanks for this. Very useful. By probing the conformational space around the model, I meant to try and predict how specific solvent conditions may (or may not) induce rearrangement, both intra and intermolecule, within an oligomeric multidomain protein compared to it in a crystalline state.
I will have an immediate look at the software and documentation you recommended and may eventually reach out for extra help. With best wishes Andre. Em qua., 24 de jun. de 2020 às 16:18, Sorin Draga <sor.dr...@gmail.com> escreveu: > 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 >> > -- 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 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/
