AMBER Archive (2009)

Subject: [AMBER] PTRAJ, rms for separated residues.

From: Catein Catherine (
Date: Mon Jun 22 2009 - 04:20:36 CDT

Dear Sir/Madam,


I could like to do use ptraj to study the rmsd of a MD simulation but include only residues 100-200 and 400-500 of a system with 600 residues.


I used the command line as follows:


rms first out rms 100-200_at_CA, 400-500_at_N1'


However, the error message about not recognized appears. Could you pls kindly instruct what command line should be used?


Best regards,




Show them the way! Add maps and directions to your party invites.
AMBER mailing list