[gmx-users] dielectric coffiecient

[shahrbanoo karbalaee]

Deat justin
thanks for your help.
I delete cl- from (peptide,tfe ,water) in my system and I see about
his charge not get message. when I add tfe in peptide (pdb2gmx -f
name.pdb -ter -ignh )the lysin amino acid is protonated (2
lysin).another charge aminoacid is D,E.do you think it related to
adding tfe to system.because my peptide charge is +1.please advise me.
and another ,do I need to define e (dielectric E) for water and tfe
in my mdp files ?or has the program  default?

best

-- 
sh-karbalaee