<br /><br /><span>On 14/06/11, <b class="name">"Marzinek, Jan" </b> <j.marzinek10@imperial.ac.uk> wrote:</span><blockquote cite="mid:787E9EFEEFC7384580812E4CA26D4F44023AC6@icexch-m4.ic.ac.uk" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span xmlns="http://www.w3.org/TR/REC-html40" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:w="urn:schemas-microsoft-com:office:word"><p>
<meta content="text/html; charset=us-ascii" http-equiv="Content-Type" />
<meta content="Microsoft Word 12 (filtered medium)" name="Generator" />
<style><!--
/* 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;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<table><tbody><tr><td lang="EN-GB" link="blue" vlink="purple"><p>
</p><div class="WordSection1">
<p class="MsoNormal">Dear Gromacs Users,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Protein SASA + ligand SASA – Protein&Ligand SASA = Interface Area between ligands protein
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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).<o:p></o:p></p>
<p class="MsoNormal">However, 10 ligands aggregates during the simulation covering their hydrophobic surface which obviously has the influence on the final interface between protein and ligands.
<o:p></o:p></p>
<p class="MsoNormal">Do you know how to calculate the interface area between all 10 ligands during the simulation time in order to subtract from final result? </p></div></td></tr></tbody></table></p></span></div></blockquote><br />Isn't this the same as the above procedure, but pairwise between ligands?<br /><br /><blockquote cite="mid:787E9EFEEFC7384580812E4CA26D4F44023AC6@icexch-m4.ic.ac.uk" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span xmlns="http://www.w3.org/TR/REC-html40" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:w="urn:schemas-microsoft-com:office:word"><p><table><tbody><tr><td lang="EN-GB" link="blue" vlink="purple"><div class="WordSection1"><p class="MsoNormal">How should I define index files?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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?
</p></div></td></tr></tbody></table></p></span></div></blockquote><br />Hydrophilic residues have more hydrogen-bonding groups than hydrophobic groups? Some indexing mis-match? The residue type labels are too simplistic?<br /><br />Mark<br /><div class="mimepart text html"><span xmlns="http://www.w3.org/TR/REC-html40" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:w="urn:schemas-microsoft-com:office:word"><p><table><tbody><tr><td lang="EN-GB" link="blue" vlink="purple"><br /></td></tr></tbody></table>
</p></span></div>