[gmx-users] protonating GLUs

Irem Altan irem.altan at duke.edu
Mon May 30 21:40:55 CEST 2016


I am trying to add an extra proton to some of the glutamates in my system. I am using pdb2gmx with the -glu flag. When I tell gmx to add an extra proton, what determines which oxygen atom will be protonated? Is it always attached to OE2, as the aminoacids.hdb file suggests? (I’m using amber03) Is there a way to attach the extra proton to OE1 instead?


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