[gmx-users] n terminal

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 29 12:23:49 CET 2008

shahrbanoo karbalaee wrote:
> thank you  justin
> in papers net  charge of peptide  is  calculated +1,with  amidated in
>  terminal. that I  defined with flag  -ter  in pdbf2gmx .and  when I
> add   tfe    in  system  I  see in  pdb  files  lys is  changed  LYSH.

OK, so your peptide has a +1 charge.  Double check this in your .top (qtot at 
the last line in the [ atoms ] section).  Then just add 1 Cl- in the solvent 
(probably best to use water) using genion.  I've gotten lost as to what the 
actual problem is any more, but if you have a +1 peptide, it seems clear to me 
that 1 Cl- belongs in your system.


> best


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


More information about the gromacs.org_gmx-users mailing list