AMBER Archive (2007)

Subject: AMBER: intra-molecular h-bonds in ptraj

From: lily ferreira (lily_1_mart_at_yahoo.fr)
Date: Thu Jan 04 2007 - 09:17:37 CST

Dear members,
                        I am triying to mesure intra-molecular bonds using ptraj. My input file is:

trajin file1.mdcrd
rms first out file1.rms :GSU_at_C1,C2,C3,C4,C5
donor MTS O1
acceptor MTS N1 H7
hbond distance 4.0 donor acceptor series hbond

but I obtain the following message

      "data was sorted, intra-residue interactions are NOT included"

    How can I list intra-molecular h-bonds?

                                                                                                        Thanking you in advance

        

        
                
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