AMBER: hbond ptraj pls help.

From: Catein Catherine <>
Date: Wed, 23 May 2007 12:56:50 +0800

Dear Sir/Madam,

I could like to do the analysis for the hbond bonds between residues LYS610
and SER720 only, but not all the LYS and SER in the PDB file. Could you
mind to let me know what is the right approach to write the ptraj file?

I tried :

donor 610.O
donor 610.N
acceptor 720.N 720.NH

But it is not recognizable by ptraj program.

I tried:

donor LYS.O
donor LYS.N
acceptor SER N NH

But ptraj tried to analysis all the LYS/SER in the file, which is too large
that not enough memory could be allocated.

Best regards,

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Received on Wed May 23 2007 - 06:07:47 PDT
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