<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
<META content="MSHTML 6.00.2800.1226" name=GENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=#ffffff>
<DIV><FONT face=Arial>I have a protein composed by two chains (36+247
aa).</FONT></DIV>
<DIV><FONT face=Arial>I have tried to use g_sas to calculate the surface only of
the light chain (36aa), </FONT></DIV>
<DIV><FONT face=Arial>so i've crated a group for this residues (365
atoms)and I've got a middle value of 125 nm^2(for the total area). </FONT></DIV>
<DIV><FONT face=Arial>This value seems to be quite constant </FONT><FONT
face=Arial>during all the simulation.</FONT></DIV>
<DIV><FONT face=Arial>I've tried to do the same calculation on some
"representative" structures with Sybyl and MolMol, </FONT></DIV>
<DIV><FONT face=Arial>selecting the same number of residues (and atoms) and I've
got a value approximatively of 2000 Ang^2.</FONT></DIV>
<DIV><FONT face=Arial>I think that this difference is very large. I'm
doing something wrong with Gromacs?</FONT></DIV>
<DIV><FONT face=Arial>I hope someone can help me</FONT></DIV>
<DIV><FONT face=Arial>Andrea</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV> </DIV>
<DIV><FONT face=Arial><BR>#############<BR>Andrea Carotti<BR>Dip.
Farmaco-chimico<BR>Università di Bari<BR>via E. Orabona, 4<BR>CAP
70124<BR>e-mail : <A
href="mailto:and.carotti@farmchim.uniba.it">and.carotti@farmchim.uniba.it</A><BR>web:
<A
href="http://www.farmchim.uniba.it/samba/">http://www.farmchim.uniba.it/samba/</A><BR>phone:
+39080/5442638<BR>fax: +39080/5442230</FONT></DIV></BODY></HTML>