detecting vanishing atoms in zero.fep

From: soroush ziaei (
Date: Thu Nov 01 2018 - 15:39:07 CDT

i have to calculate solvation free energy ( third part of tutorial ) in
order to achieve delta<g> for compare the solvation between two structure.
I have showed topology file recently (generated with cgenff & swiss param
server). this structure has a symmtry similar to hybrid molecule in
tutorial file & i want to know how can i detect which atoms should be -1,1
or 0 ?!
my prespective ( according to the fep file that already exist in tutorial
with symmetry in some groups ) is:
 first, i have to change the value of one side to 1 and the up side
(similar to tutorial) to -1, doesn't it?
if my guess is almost correct, then why after changing value of one side to
1, the running of fep for backward faced to an error? [rm, can not remove
eq3.restart; no such file or directory]!

i appreciate,
please guide me.

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