Dear Sir/Madam:
I apply MD simulation to investigate fXa which is a protein-ligand complex. I got the result file. When analyzing the results, I have some problems. I want to use AMBER14 program do hydrogen bonding analysis, but there exist some error, as shown in the following:
Error: 'donor' is deprecated.
Hydrogen bond acceptors and donors are defined within the 'hbond' action.
Error: Unrecognized character in expression: :
'donor mask :GLN.OE1': Invalid command or expression.
1 errors encountered reading input.
command: cpptraj complex.top < analyse_hbond.ptraj > analyse_hbond.out. I use the ptraj script named analyse_hbond.ptraj (see appendix). I hope for an early answer to my question. Thank you!
Sincerely,
Liyan
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Received on Fri Jun 24 2016 - 05:00:02 PDT
