Joe Joe wrote:
I think there is a tdb problem when using pdb2gmx on a single amino
acid. The tdb databases replaces the CA with different charges depending
on whether its a c or n termini. When its a single amino acid you get
the c terminal charge and thus the overall charge is incorrect. Am I
missing something?
That will depend somewhat on which force field you're using. A quick look at
ffG53a6-n/c.tdb indicates there should be no conflict; CA is only replaced in
the -n.tdb file, there is no competing CA replacement in -c.tdb. In OPLS, you
just have to be sure you're choosing the zwitterion form for each terminus
(since you have a zwitterionic single amino acid), or else you will get conflict.
-Justin
Thanks,
Ilya
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 gmx-users@gromacs.org
http://lists.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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
