Greetings to all,
I have been playing with the nativecontacts and hbond commands because I am trying to figure out the number of types of contacts between a protein and graphene oxide surfaces. Many contacts are formed that are nonnative, but I cannot seem to exact information about the identities of these contacts.
I will try to explain as best as I can as follows:
For example, I use the command
"nativecontacts :1-22 :23-1030 distance 3.0 byresidue resout contactsbyres.dat"
I get a list of the native contacts by residue and the fraction of frames that the residues are within 3.0.
When I use the command
nativecontacts :1-22 :23-1030 distance 3.0 out contacts.dat"
I get a list of number of native contacts (atoms) and non native contacts (atoms).
I cannot figure out how I could get an output similar to the contactsbyres.dat, but with both the native and nonnative contacts. Is this possible with cpptraj?
If not, is there another way for me to determine this?
Thanks in advance for your help.
Best, Kristin
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Received on Thu Mar 24 2016 - 10:30:04 PDT
