Dear all,
I want to analyze the number of contact points between RNA and polymer in the RNA-polymer complex from the trajectory.
I try contacts in ptraj:
contacts first out contacts.out time 2 distance 3.0 :MOL
MOL is the name of polymer.
I get the following results:
#time Contacts native Contacts
2.00 798 798
4.00 804 784
6.00 824 794
8.00 814 786
10.00 814 782
12.00 812 784
14.00 828 788
16.00 806 776
18.00 812 788
-----
At the beginning the polymer is over 3 angstrom away from RNA. I think native contacts is inter-molecule contact number.
So, the final contacts = Contacts - native Contacts
#time Final Contacts
2.00 0
4.00 20
6.00 30
8.00 28
10.00 32
12.00 28
14.00 40
16.00 30
18.00 24
-----
I am not sure if my analysis is right. Could anyone give me the advices?
Regards,
Ouyang
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Received on Fri May 29 2009 - 01:09:06 PDT
