Hello,
I want to study hydrogen bonds between two proteins and also between
protein–water–protein, i.e. bridging water molecules between the two
proteins.
To my delight I found in the AmberTools12 manual that CPPTRAJ had
exactly that functionality in the hbond command, with the arguments
solventdonor, solventacceptor, solvout and bridgeout. However, when I
run CPPTRAJ with those arguments to hbond they are ignored, and when I
look in the code, it seems that they are not even implemented.
Is this so? Do these commands exists in some developmental version
that I can get my hands on? Or is it possible do the analysis in some
other way either with CPPTRAJ or PTRAJ?
Best regards,
Samuel
Researcher
Department och Chemistry and Molecular Biology
University of Gothenburg
Sweden
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Received on Wed Aug 29 2012 - 08:00:03 PDT
