Hsin-Lin Chiang wrote:
Hi ,Mark:
I had announced my system is a dimer with each peptides have 6 residues.
I'm sorry if I didn't express it to be understood easily.
Can you please tell me why 13 coils are reasonable if my systems is a
dimer?
It's not. I already answered this:
http://lists.gromacs.org/pipermail/gmx-users/2010-May/051311.html
-Justin
regards,
Hsin-Lin
Hi, Justin:
I post my coordinate with protein translated by trjconv
By this gro file, I get 0 structure and 13 coils.
Haven't you been saying for what seems like weeks now that you have 12
residues in your "protein"? If so...
C 70 2.223 2.893 1.484 -0.0883 0.1244 -0.1837
6ASN O1 71 2.111 2.941 1.505 -0.2557
-0.4837 -0.1041
6ASN O2 72 2.313 2.953 1.419 -
0.5561 0.0660 0.4455
Here, there's quite clearly an internal COO and NH3... hence it seems
that you have two 6-residue chains. That's important data to be aware
of, and to communicate to people who might help... Our belief that you
really had a 12-residue peptide excludes this kind of issue from
trouble-shooting, which ends up wasting everyone's time.
Mark
--
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 listgmx-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
