The Schrodinger software suite may also have a module that you can use (https://www.schrodinger.com/platform#product-list-collapse). You can contact technical help for advice.
Daniel On Wed, Jun 24, 2020 at 7:54 PM Andre LB Ambrosio <an...@ifsc.usp.br> wrote: > 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 > ######################################################################## 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/
