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I turned off all non bonded interaction using the following:<BR>
<BR>
energygrp_excl = SOL SOL SOL Protein_A SOL Protein_B Protein_A Protein_B<BR>
<BR>
(where Protein_A and Protein_B, are the 2 molecules (peptides) in the box)<BR>
I assume this will not affect excluded volume i.e I do not expect to see distances less that twice the radius of an atom.<BR>
However, after my simulation I get the ff result for the distance between 2 alpha C atoms in Protein_A and Protein_B (using g_dist):<BR>
<TABLE style="WIDTH: 48pt; BORDER-COLLAPSE: collapse" cellSpacing=0 cellPadding=0 width=64 border=0 x:str>
<COLGROUP>
<COL style="WIDTH: 48pt" width=64>
<TBODY>
<TR style="HEIGHT: 12.75pt" height=17>
<TD style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; WIDTH: 48pt; BORDER-BOTTOM: #ece9d8; HEIGHT: 12.75pt; BACKGROUND-COLOR: transparent" align=right width=64 height=17 x:num="0.18281130000000001"><FONT face=Arial color=#000000>0.182811</FONT></TD></TR>
<TR style="HEIGHT: 12.75pt" height=17>
<TD style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; BORDER-BOTTOM: #ece9d8; HEIGHT: 12.75pt; BACKGROUND-COLOR: transparent" align=right height=17 x:num="0.22101419999999999"><FONT face=Arial color=#000000>0.221014</FONT></TD></TR>
<TR style="HEIGHT: 12.75pt" height=17>
<TD style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; BORDER-BOTTOM: #ece9d8; HEIGHT: 12.75pt; BACKGROUND-COLOR: transparent" align=right height=17 x:num="0.240868"><FONT face=Arial color=#000000>0.240868</FONT></TD></TR>
<TR style="HEIGHT: 12.75pt" height=17>
<TD style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; BORDER-BOTTOM: #ece9d8; HEIGHT: 12.75pt; BACKGROUND-COLOR: transparent" align=right height=17 x:num="0.27928229999999998"><FONT face=Arial color=#000000>0.279282</FONT></TD></TR>
<TR style="HEIGHT: 12.75pt" height=17>
<TD style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; BORDER-BOTTOM: #ece9d8; HEIGHT: 12.75pt; BACKGROUND-COLOR: transparent" align=right height=17 x:num="0.32229079999999999"><FONT face=Arial color=#000000>0.322291</FONT></TD></TR>
<TR style="HEIGHT: 12.75pt" height=17>
<TD style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; BORDER-BOTTOM: #ece9d8; HEIGHT: 12.75pt; BACKGROUND-COLOR: transparent" align=right height=17 x:num="0.33432499999999998"><FONT face=Arial color=#000000>0.334325</FONT></TD></TR>
<TR style="HEIGHT: 12.75pt" height=17>
<TD style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; BORDER-BOTTOM: #ece9d8; HEIGHT: 12.75pt; BACKGROUND-COLOR: transparent" align=right height=17 x:num="0.35699140000000001"><FONT face=Arial color=#000000>0.356991</FONT></TD></TR>
<TR style="HEIGHT: 12.75pt" height=17>
<TD style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; BORDER-BOTTOM: #ece9d8; HEIGHT: 12.75pt; BACKGROUND-COLOR: transparent" align=right height=17 x:num="0.35727330000000002"><FONT face=Arial color=#000000>0.357273</FONT></TD></TR>
<TR style="HEIGHT: 12.75pt" height=17>
<TD style="BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: #ece9d8; BORDER-BOTTOM: #ece9d8; HEIGHT: 12.75pt; BACKGROUND-COLOR: transparent" align=right height=17 x:num="0.40196490000000001"><FONT face=Arial color=#000000>0.401965</FONT></TD></TR></TBODY></TABLE><BR>
....<BR>
The diameter of a C atom is about .3nm so I was surprised to see distances less than that.<BR>
I'll appreciate any help.<BR>
<BR>
Regards<BR>
John<BR>
<BR>
<BR>
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