Dear Sir/Madam,
I could like to calculate the occurence of a protein residue within a 5 A cutoff of the drug at each time step. So,
I did the ptraj analysis as follows. Here is my input file.
==================================================
trajin xxx.mdcrd.gz
rms first :1-22.CA, :23-24.N1
contacts first byresidue out xxx distance 5.0 :1-22.CA, :23-24.N1
==================================================
I got two files xxx and xxx.native. What is the different between these two files in meaning?
I found both files are in the same format.
==================================================
#time residue0 residue1......residue24
1 2 5 11
2 3 6 21
3
4
..................
==================================================
What is the meaning of the numbers in the table? No of contact or residue nuber?
For the 2nd data in the 2nd row of the result table. Should I interpret residue0 at time 1 has two contacts or has closest contact with residue2?
Please kindly help.
Are there any method I can use to determine the no and indentity of contact residues with the drugs during the xxx.mdcrd trajectory?
Best regards,
Cat
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Received on Wed May 26 2010 - 01:30:55 PDT
