[gmx-users] g_sas index files/hydrogen bonds

[Mark Abraham]

On 14/06/11, "Marzinek, Jan"  <j.marzinek10 at imperial.ac.uk> wrote:
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> Dear Gromacs Users,
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> I am calculating the hydrophobic interface area using g_sas between ligands (their hydrophobic solvent accessible surface area (SASA) >95%) and hydrophobic residues of coiled coil fragment of protein (two helical strands) as follows:
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> Protein SASA + ligand SASA – Protein&Ligand SASA = Interface Area between ligands protein
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> I obtained the hydrophobic interface area increasing during the simulation time -> so everything seems to be ok, because from my simulation 10 ligands occupy hydrophobic residues (the helical terminal strands open allowing ligands to come
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> However, 10 ligands aggregates during the simulation covering their hydrophobic surface which obviously has the influence on the final interface between protein and ligands.
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> Do you know how to calculate the interface area between all 10 ligands during the simulation time in order to subtract from final result? 
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Isn't this the same as the above procedure, but pairwise between ligands?


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> How should I define index files?
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> The second question: I also calculated the hydrogen bonds between ligands and the protein. What is interesting: app. 70% of hydrogen bonds between hydrophobic ligands are formed with HYDROPHILIC residues of protein. Any clue what is happening
>  as final conformation involve ligands between hydrophobic surfaces of the protein?
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Hydrophilic residues have more hydrogen-bonding groups than hydrophobic groups? Some indexing mis-match? The residue type labels are too simplistic?

Mark









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