On 14/06/11, "Marzinek, Jan" <[email protected]> wrote: > > > > > > <!-- > /* Font Definitions */ > @font-face > {font-family:"Cambria Math"; > panose-1:2 4 5 3 5 4 6 3 2 4;} > @font-face > {font-family:Calibri; > panose-1:2 15 5 2 2 2 4 3 2 4;} > /* Style Definitions */ > p.MsoNormal, li.MsoNormal, div.MsoNormal > {margin:0cm; > margin-bottom:.0001pt; > font-size:11.0pt; > font-family:"Calibri","sans-serif";} > a:link, span.MsoHyperlink > {mso-style-priority:99; > color:blue; > text-decoration:underline;} > a:visited, span.MsoHyperlinkFollowed > {mso-style-priority:99; > color:purple; > text-decoration:underline;} > span.EmailStyle17 > {mso-style-type:personal-compose; > font-family:"Calibri","sans-serif"; > color:windowtext;} > .MsoChpDefault > {mso-style-type:export-only;} > @page WordSection1 > {size:612.0pt 792.0pt; > margin:72.0pt 72.0pt 72.0pt 72.0pt;} > div.WordSection1 > {page:WordSection1;} > --> > > > > > > > > > Dear Gromacs Users, > > > > > > 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: > > > > > > Protein SASA + ligand SASA – Protein&Ligand SASA = Interface Area between > ligands protein > > > > > > > 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 > inside the protein). > > > However, 10 ligands aggregates during the simulation covering their > hydrophobic surface which obviously has the influence on the final interface > between protein and ligands. > > > > Do you know how to calculate the interface area between all 10 ligands during > the simulation time in order to subtract from final result? > > > > >
Isn't this the same as the above procedure, but pairwise between ligands? > > > > > How should I define index files? > > > > > > 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? > > > > > > 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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