AMBER Archive (2009)

Subject: [AMBER] contacts in ptraj

From: 欧阳德方 (ouyangdf1978_at_hotmail.com)
Date: Thu May 28 2009 - 06:55:28 CDT


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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