Dear All,
How to determine the SASA of different ligands in absolute values and percentage of their potential SASA in solution to estimate how buried they are in GROMACS.
Thank you in advance.
Well, Vikram Dalal , I would run a separate simulation of your ligand in water at the same salt concentration. I would calculate the average SASA for the ligand in water. Then I would calculate SASA from your protein ligand-simulation. Afterward, I would import the xmgrace data into python using commands like this:
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####### file input #####################
# importing the ligand in wate SASA data
with open("directory/ligand_water_sasa.xvg") as f:
for line in f:
cols = line.split()
if len(cols) == 2:
ligand_water_sasa_x1.append(float(cols[0]))
ligand_water_sasa_y1.append(float(cols[1]))
# importing the ligand with protein SASA data
with open("directory/ligand_protein_sasa.xvg") as f:
for line in f:
cols = line.split()
if len(cols) == 2:
ligand_protein_sasa_x1.append(float(cols[0]))
ligand_protein_sasa_y1.append(float(cols[1]))
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Then I'd use numpy commands to divide the protein-ligand SASA measurement by the ligand-water SASA to get the percentage of absolute SASA. Afterward, I'd plot the results using the matplotlib python module.
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