AMBER Archive (2004)

Subject: AMBER: Error while protonating a PDB file

From: Mike (amber_list_at_speedpost.net)
Date: Thu Mar 25 2004 - 17:47:54 CST

Hi AMBERites,

I got an error while using 'protonate' on a PDB file.

The command i gave was

protonate -k -d $AMBERHOME/dat/PROTON_INFO < my.pdb > my.H.pdb

The error message is

 error in finding unit vector:
    1 3 51.060 -11.635 48.664 51.060 -11.635 48.664
error: case #1.100b, bond r2 has zero length.
ip= 2 na= 3 nhyd= ***** protp(1-3,1-4)= 51.21 52.74 52.20
0.00-10.28-10.74-10.19 0.00 50.29 49.58 37.23 0.00

Can anybody please tell me what this error means and what should i do to
rectify?

Thanks in advance
Mike 

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