Dear All,
I am trying to use the AMBER umbrella sampling method to get the free energy of transfer profile for a substrate molecule through a channel protein. And I have referred
https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial , but several problems have trapped me due to my system is different. 1) If I put one substrate molecule close to the protein channel entrance, how can I define its location, I mean such as Z=0(need it to get r2=? in the pull.RST); 2) Also the distance restraint file, I use igr1=substrate atom number, how should I difine igr2=? use residue near the protein channel exit? If yes, use one or several?
Any suggestions would be greatly appreciated.Thank you in advance!
All the best,
Wu Meng
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 13 2017 - 03:00:03 PDT
