Hi, I am wondering how did this panel do the alignment when using the first frame as the reference structure? Based on CA, backbone, side chain or...? Thanks!
Hi, very nice video tutorials. Thanks for it. I have following questions: is it possible to do a QM/MM simulation also of a protein-ligand system as easily as demonstrated in these Desmond videos? Also kindly let me know if free energy of binding can be straightway calculated using Desmond.
Hi Sinha Suman, Thanks for your comment. Yes, you can do a QM/MM simulation of protein-ligand systems using Schrödinger's program QSite (www.schrodinger.com/QSite/). We don't currently have any video tutorials for QSite, however, the QSite User Guide contains detailed information including a tutorial. It is available via Maestro or from www.schrodinger.com/supportdocs/ Once opened within Maestro the QSite panel quick help button also contains details on how to set up and use the panel. Best regards, Jarred
![[OUTDATED] Desmond - Preparing a Protein for MD Simulations (Part 1)](http://i.ytimg.com/vi/-i5MIbUJKD8/mqdefault.jpg)
![[OUTDATED] Desmond - Preparing a Protein for MD Simulations (Part 1)](/img/tr.png)
Please see learn.schrodinger.com/private/edu/release/current/Documentation/html/tutorials/desmond_intro/desmond_intro.htm? for updated steps.
Hi, I am wondering how did this panel do the alignment when using the first frame as the reference structure? Based on CA, backbone, side chain or...? Thanks!
How many configurations of pc is needed to do MD? My pc configuration is cori5,4gp ram 1tera rom. And the operating system is windows 10
is there a way to do the analysis through command line on linux?
Can I analyze a NAMD MD trayectory (.dcd) with Desmond?
Hi, very nice video tutorials. Thanks for it. I have following questions:
is it possible to do a QM/MM simulation also of a protein-ligand system as easily as demonstrated in these Desmond videos? Also kindly let me know if free energy of binding can be straightway calculated using Desmond.
Hi Sinha Suman,
Thanks for your comment. Yes, you can do a QM/MM simulation of protein-ligand systems using Schrödinger's program QSite (www.schrodinger.com/QSite/). We don't currently have any video tutorials for QSite, however, the QSite User Guide contains detailed information including a tutorial. It is available via Maestro or from www.schrodinger.com/supportdocs/ Once opened within Maestro the QSite panel quick help button also contains details on how to set up and use the panel.
Best regards,
Jarred
Hi! Is it possible to convert a gromacs trajectory file (.xtc) into a .cms file, in order to analyze it with desmond?
it is possible ????