[gmx-users] dielectric coffiecient

shahrbanoo karbalaee shahrbanoo at gmail.com
Tue Oct 28 10:09:18 CET 2008

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?



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