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.
-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
========================================
_______________________________________________
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
