----- Original Message ----- From: Hsin-Lin Chiang <jian...@phys.sinica.edu.tw> Date: Thursday, May 27, 2010 0:28 Subject: [gmx-users] Re: the output of do_dssp To: gmx-users@gromacs.org
> 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... <snip> > 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 > 7LEU > N 73 1.111 2.804 > 2.186 0.3062 -0.5955 -0.0550 > 7LEU H1 > 74 1.174 2.856 2.129 > 0.2303 -0.3221 0.1077 > 7LEU H2 > 75 1.019 2.834 2.164 > 0.0461 -1.9085 -0.8807 > 7LEU H3 > 76 1.126 2.815 2.284 > 0.4122 -2.4532 0.1866 <snip> -- 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
