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<DIV><FONT face=Arial size=2>Hello Alok,</FONT></DIV>
<DIV><FONT face=Arial size=2> Try to follow
this order, before the energy minimization, where ache is the name of your pdb
file:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT size=2>
<P>pdb2gmx -f ache.pdb -o ache.gro -p ache.top</P><FONT size=2>
<P>editconf -bt cubic -f ache.gro -o ache.gro -c -d 0.65</P><FONT size=2>
<P>genbox -cp ache.gro -cs spc216.gro -o ache_st.gro -p ache.top</P><FONT
size=2>
<P>make_ndx -f ache</P></FONT>
<P><FONT face=Arial></FONT> </P>
<P><FONT face=Arial></FONT> </P>
<P><FONT
face=Arial>
Arlan da Silva Gonçalves</FONT></P>
<P> </P></FONT>
<P><FONT face=Arial></FONT> </P></FONT>
<P><FONT face=Arial></FONT> </P></FONT></DIV></BODY></HTML>