AMBER Archive (2007)

Subject: AMBER: hbond ptraj pls help.

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Tue May 22 2007 - 23:56:50 CDT

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_at_O
donor 610_at_N
acceptor 720_at_N 720_at_NH

But it is not recognizable by ptraj program.

I tried:

donor LYS_at_O
donor LYS_at_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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