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<DIV>1- editconf -f p.gro -o p.gro -bt cubic -c -d 0.7<BR>2- genbox -cp p.gro
-cs spc216.gro -o p.gro -p p.top<BR>my peptides have diferent structure , and
then my BOX <BR>and my number of H2O are diferent, my question is<BR>hOW COULD
I GENERATE exactly the same number of solvent <BR>molecules and box
size.</DIV>
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<DIV><FONT face=Arial size=2>include the solvent in your SA. I did that too with
gromacs. It works</FONT></DIV>
<DIV><FONT face=Arial size=2>fine. And don't need a big box for 11 residues.
</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>The implicit solvent SA I used before was with
CHARMM implemented</FONT></DIV>
<DIV><FONT face=Arial size=2>in the lab by. S. Hassan. Can write him a
message at</FONT></DIV>
<DIV><FONT face=Arial size=2><A
href="mailto:mago@inka.mssm.edu">mago@inka.mssm.edu</A> you'll need CHARMM
though</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>XAvier</FONT></DIV></BODY></HTML>