<div class="im" style>Dear Bipin,</div><div class="im" style>Edit your topology file as:</div><div class="im" style><br></div><div class="im" style>###########################################</div><div class="im" style>; Include forcefield parameters<br>
#include "amber99sb-ildn.ff/forcefield.itp"<br></div><div class="im" style><font color="#222222" face="arial, sans-serif"><br></font><font color="#500050" face="arial, sans-serif">; Include chain topologies</font><br>
<font color="#500050" face="arial, sans-serif">#include "topol_Protein_chain_A.itp"</font><br><font color="#500050" face="arial, sans-serif">#include "topol_Ion_chain_A2.itp"</font></div><div class="im" style>
<font color="#500050" face="arial, sans-serif"><br></font><span style="font-size:13px;color:rgb(34,34,34);font-family:arial,sans-serif"><b>#include "oct.itp"</b></span></div><div class="im" style><br style="font-size:13px;color:rgb(34,34,34);font-family:arial,sans-serif">
<font color="#500050" face="arial, sans-serif">; Include water topology</font><br><font color="#500050" face="arial, sans-serif">#include "amber99sb-ildn.ff/tip3p.itp"</font><br><br><font color="#500050" face="arial, sans-serif">#ifdef POSRES_WATER</font><br>
<font color="#500050" face="arial, sans-serif">; Position restraint for each water oxygen</font><br><font color="#500050" face="arial, sans-serif">[ position_restraints ]</font><br><font color="#500050" face="arial, sans-serif">; i funct fcx fcy fcz</font><br>
<font color="#500050" face="arial, sans-serif"> 1 1 1000 1000 1000</font><br><font color="#500050" face="arial, sans-serif">#endif</font><br><br><font color="#500050" face="arial, sans-serif">; Include topology for ions</font><br>
<font color="#500050" face="arial, sans-serif">#include "amber99sb-ildn.ff/ions.itp"</font><br><br><font color="#500050" face="arial, sans-serif">[ system ]</font><br><font color="#500050" face="arial, sans-serif">; Name</font><br>
<font color="#500050" face="arial, sans-serif">Protein in water</font><br><br><font color="#500050" face="arial, sans-serif">[ molecules ]</font><br><font color="#500050" face="arial, sans-serif">; Compound #mols</font><br>
<font color="#500050" face="arial, sans-serif">Protein_chain_A 1</font><br><font color="#500050" face="arial, sans-serif">Ion_chain_A2 1</font><br></div><div class="im" style><b><span style="font-size:13px;color:rgb(34,34,34);font-family:arial,sans-serif">1-octanol 1</span><br style="font-size:13px;color:rgb(34,34,34);font-family:arial,sans-serif">
</b></div><span style><b>SOL 8987</b></span><div><span style>#######################################</span></div><div><span style><br></span></div><div><font color="#222222" face="arial, sans-serif">It may be helpful to you.</font></div>
<div><font color="#222222" face="arial, sans-serif"><br></font></div><div><font color="#222222" face="arial, sans-serif">Biswajit</font></div>