Hi,<br><div class="gmail_quote"><br>The specific thing we're trying to achieve here (in this case) is add a flat bottom distance restraint between an atom in the ligand and a virtual site in the center of a protein binding site. Not sure if that can be achieved with the pull code?<br>
<br>We are also (separately) interested in having distance, angle, and dihedral restraints between reference atoms in the ligand and reference atoms in the protein. These restraints need to be lambda dependent, and ideally we would like to be able to use them with decoupling (again, currently not possible). Is the pull code flexible enough to be able to do angle and dihedral restraints somehow? (There is a fairly specific set of restraints we need for technical reasons -- one distance, two angles, three torsions. Other forms won't get us what we need...).<br>
<br>Thanks.<br><br><br><div class="gmail_quote">On Thu, Jun 23, 2011 at 4:23 AM, Berk Hess <span dir="ltr"><<a href="mailto:hess@cbr.su.se" target="_blank">hess@cbr.su.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<u></u>
<div text="#000000" bgcolor="#ffffff">
Hi,<br>
<br>
You can manually set up the decoupling, but that's very tedious and
error prone.<br>
I think the best procedure would be to restrain using the pull code,<br>
but I don't know if that's currently flexible enough to cover most
cases.<br>
If not, we should think about extend the functionality of the pull
code.<br>
<br>
I though the decoupled state is described somewhere in the manual.<br>
It is a non-periodic state with pure Coulomb and LJ interactions
without cut-offs<br>
(unless you use couple-intramol).<br><font color="#888888">
<br>
Berk</font><div><div></div><div><br>
<br>
On 06/23/2011 04:46 AM, David Mobley wrote:
<blockquote type="cite">Hi,
<div><br>
</div>
<div>We're trying to do absolute binding free energy calculations
using Michael Shirts' latest free energy code (to be included in
4.6 if I understand correctly; right now it's a branch of 4.5).
These require using a restraint between the protein and the
ligand, which currently we're doing using virtual sites. I am
interested in also doing these calculations using "decoupling",
wherein internal interactions of the perturbed molecule (in this
case the ligand) are retained. This involves something like the
following in the mdp file:</div>
<div><br>
</div>
<div>
<span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">couple-moltype
= MOL<br>
couple-lambda0 = vdw-coul<br>
couple-lambda1 = none<br>
</span><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">couple-intramol
= no</span></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br>
</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse">if,
for example, the ligand is a molecule named 'MOL'.<br clear="all">
</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br>
</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse">My
question is this: Is there any way to get this to work when
the ligand and the protein are part of the same "molecule"?
Specifically, to have restraints betweeen the protein and
the ligand (such as using a virtual site) which are
NECESSARY for absolute binding free energy calculations, I
must have the protein and ligand as part of the same
molecule (unless there's a workaround I'm not aware of). But
to get decoupling to work using the above I seem to need to
have the protein and ligand as separate molecules,
suggesting they are incompatible. Is there a workaround I'm
not aware of?</span></font></div>
<div><br>
</div>
<div>Also, on a related note -- when decoupling is done, what is
the end state for the decoupled object? Is it the decoupled
object in gas phase in a periodic system (interacting with
copies of itself), or in a nonperiodic system? </div>
<div><br>
</div>
<div>Thanks!</div>
<div><br>
</div>
<div>-- </div>
<div>David Mobley<br>
<a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a><br>
<a href="tel:504-383-3662" value="+15043833662" target="_blank">504-383-3662</a><br>
<br>
<br>
</div>
</blockquote>
<br>
</div></div></div>
<br>--<br>
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Department of Chemistry<br>
University of New Orleans<br><a href="mailto:dlmobley@uno.edu" target="_blank">dlmobley@uno.edu</a><br>ph. <a href="tel:504-383-3662" value="+15043833662" target="_blank">504-383-3662</a><br>fax <a href="tel:504-280-6860" value="+15042806860" target="_blank">504-280-6860</a><br>
<br><br>
<br></div><br><br clear="all"><br>-- <br>David Mobley<br><a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a><br>504-383-3662<br><br><br>