Dear Amber users,
I am trying to build a membrane protein system. These are the steps I
followed:
1. I built the bilayer by CHARMM-GUI and equilibrated it in Amber. I
stripped the waters provided by CHARMM-GUI.
2. Then I aligned the protein on top of the membrane by VMD.
Now, when I try to solvate the system, I am not able to put water only
above and below the lipid. I know that CHARMM-GUI may provide me with a
solvated lipid but since my protein is only present in the upper leaflet on
the lipid, I wish to put unequal amounts of water with more water on top of
lipid.
So, I was just wondering if any of you have done something similar and
could provide me with some suggestions about how do I solve this simple yet
tricky problem.
Thanks in advance.
Regards,
Souvik
----------------------------------------------------------
Souvik Dey
Graduate Student
Department of Chemistry
University of Illinois Chicago
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 03 2019 - 18:30:01 PST
