[gmx-users] error in solvation

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 5 11:48:42 CEST 2008

shahrbanoo karbalaee wrote:
> Dear justin
> I hope u r ok.I make tfe 30%in water with genconf and genbox.after
> that I minmized and equilbrated this mix solvent for 14ps.and with
> command trjconv got the last pdb file.this file (last pdb file)was
> solvated.gro(editconf).now I want to  insert peptide in solvated.gro
> but donot insert  molecules  tfe and spc in box.what do i do?

The tool to solvate structures is genbox:

genbox -cp peptide.gro -cs solvated.gro

...although you may not end up with 30% TFE, depending on which molecules get 


> thanks


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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