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<p class=MsoNormal>Dear GROMACS users,<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal>I am investigating a certain peptide which is well bound to
some protein; their configuration is known from the PDB.<o:p></o:p></p>

<p class=MsoNormal>My aim is to compare the binding free energies of several variants
of the peptide.<o:p></o:p></p>

<p class=MsoNormal>In particular, I wish to mutate some amino acids to others.<o:p></o:p></p>

<p class=MsoNormal>I have read some tutorials and mailing list messages; still,
I have several questions unanswered.<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal>I plan to use the Thermodynamic Integration (TI) method in
an &#8220;alchemical&#8221; setting, in which I &#8220;turn off&#8221; the side
chain.<o:p></o:p></p>

<p class=MsoNormal>The &#8220;naked&#8221; amino acid will then be my reference
point comparing to real amino acids.<o:p></o:p></p>

<p class=MsoNormal>In this way I should be able to obtain, using the usual
thermodynamical cycle, the binding free energy difference of two amino acids
(Delta Delta G), which is sufficient for my needs and should be more accurate
than computing absolute binding free energies (Delta G).<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal>1) Does this sound like the best approach?<o:p></o:p></p>

<p class=MsoNormal>2) In particular, is it O.K. to use a &#8220;naked&#8221;
amino acid (with no side chain at all) as the reference, or should Glycine or
Alanine be used?<o:p></o:p></p>

<p class=MsoNormal>3) Following the above procedure, I still would not achieve a
&#8220;naked&#8221; amino acid.<o:p></o:p></p>

<p class=MsoNormal>&nbsp;&nbsp;&nbsp;&nbsp; Rather, a side chain &#8220;ghost&#8221;
remains, non-interacting but still bonded to itself and to the C-alpha.<br>
&nbsp;&nbsp;&nbsp;&nbsp; Is it correct to assume that the contribution of such
a &#8220;ghost&#8221; would cancel between the free and bound peptide?<o:p></o:p></p>

<p class=MsoNormal>4) Are the OPLS-AA force field, theTIP-3P water model and
the NpT ensemble good choices?<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal>I have seen two methods used to make the change between the
initial and final states.<o:p></o:p></p>

<p class=MsoNormal>The first (and simplest) is to use the couple-moltype parameter
of mdrun.<o:p></o:p></p>

<p class=MsoNormal>However, this seems to change a whole molecule, while I&#8217;m
interested in changing only a part (the side chain).<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal>5) Can I define the side chain and the amino acid backbone
as different molecules, and change the former, still connecting them one to the
other?<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal>Alternatively, the topology of the B state can be explicitly
provided (as described e.g. in section 5.7.4 of the version 4.0 user manual).<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal>6) The atom charges can be specified for state B, as
appropriate for turning off the Coulomb interactions.<o:p></o:p></p>

<p class=MsoNormal>&nbsp;&nbsp;&nbsp;&nbsp; In order to turn off the vdW ones, must
I define new atom types?<o:p></o:p></p>

<p class=MsoNormal>7) Are there perhaps such amino acid variants already built?
<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal>Finally, some technicalities:<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal>8) I have seen the sc-alpha parameter (when sc-power = 1) given
the values 1.0, 0.7 and 0.5. What is recommended?<o:p></o:p></p>

<p class=MsoNormal>9) Should I employ DispCorr = EnerPres ?<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<p class=MsoNormal>Thanks,<o:p></o:p></p>

<p class=MsoNormal>Ehud Schreiber.<o:p></o:p></p>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

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