All, I'm using do_dssp to do some secondary structure analysis. I have a peptide with two nonstandard residues, one at the N-terminus and one at the C-terminus, and a total of N residues. The output of do_dssp only contains information on N-2 residues (numbered 1 through N-2) while my trajectory input contains information on the full N residues. I'm guessing this is because dssp doesn't know how to calculate secondary structure for nonstandard residues, and so it simply omits the two nonstandard residues and then numbers the remaining residues consecutively beginning at 1. Is this correct?
Thanks, David _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
