shahrbanoo karbalaee wrote:
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?
If your peptide has a net charge of +1, then you need a counterion to neutralize
the charge. But I'm confused. If you have 2 Lys and an Asp and Glu, then the
net charge should be 0, unless you've done something strange with your termini.
There is no need to set a dielectric, at least not with PME for electrostatics.
If you're using reaction field, then you would specify a dielectric beyond a
certain cut-off.
-Justin
best
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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