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