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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
