[AMBER] cpptraj surf

From: George Tzotzos <gtzotzos.me.com>
Date: Fri, 24 Aug 2012 15:22:01 +0200

For the calculation of SASA of a protein or ligand (uncomplexed) does one need the solvated coordinate files?

trajin prod_10ns.mdcrd
surf SASA :1-125 out protein_trj.dat

#Frame SASA
       1 7029.6526
       2 7136.5578 ..... etc.

Changing the above mask to :126 (ligand) produced

#Frame SASA
       1 60.1000
       2 68.6019....etc

I used effectively the same script changing trajin to ligand.inpcrd and protein.inpcrd (coordinates of the unsolvated starting structures)

The ligand output was

#Frame SASA
       1 350.8079

whereas the protein

#Frame SASA
       1 6635.1916

In terms of the ligand, the above matches what has been reported in the literature (ligand effectively buried). I have difficulties interpreting the situation with the protein. I would expect that the proteins SASA during the time evolution of the trajectory would be less than that of the apoprotein.

Any suggestions regarding this above would be most helpful.



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Received on Fri Aug 24 2012 - 06:30:03 PDT
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