AMBER Archive (2009)

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

From: Catein Catherine (askamber23_at_hotmail.com)
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,

 

Cat

 

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