<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi,</div><div><br></div><div>I hacked the pull code to work in the direction of a helical reaction coordinate. In the special case of helix pitch == 0 you get angular or torsional restraints. It could probably do with further generalisation, but at least it's a starting point if anyone's interested.</div><div><br></div><div>Erik</div><br><div><div>On 21 Jun 2013, at 22:44, David Mobley <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Hi,<br><br>Anyone have any insights on this? Do we need to think about implementing angle/torsional restraints in the pull code, or can we re-cast the restraints available within topology files to use absolute atom numbering?<br>
<br>Thanks.<br><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Jun 14, 2013 at 12:47 PM, David Mobley <span dir="ltr"><<a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hi, devs,<br><br></div><div>I'm writing with an issue relating to the interplay of new free energy features with restraints.<br>
</div><div><br></div>I'm very much appreciating some of the new free energy features in gromacs, such as the 'couple-moltype' option which provides a way to set up decoupling or annihilation of a specific molecule via free energy calculations without having to edit the topology file directly. This is especially great when it comes to decoupling -- charge decoupling was not previously possible via topology file editing, and vdW decoupling took substantial manipulation of the topology file.<br>
<br>However, for binding free energies, my work employs orientational restraints between the protein and ligand. I need to be able to impose both dihedral and angle restraints on angles between the protein and ligand. Currently, I do this using angle-restraints and dihedral-restraints. This requires that both the protein and ligand be within the same logical 'molecule', which (unfortunately) means that I can't make use of the new free energy features above, since couple-moltype has to apply to a whole molecule, not just part of a molecule.<br>
<br></div>So, my I see two possible solutions to the problem, and hence have these questions:<br>1) Can dihedral and angle restraints be applied via the pull code? If not, are there any plans to add that?<br></div>2) Alternatively, what about modifying the restraints code so it uses (or at least optionally allows) absolute atom numbering, rather than numbering within a specific molecule, thus allowing restraints (angle-restraints and dihedral-restraints) to be applied between 'molecules'?<br>
<br></div>Thanks!<span class="HOEnZb"><font color="#888888"><br>David<br><br clear="all"><div><br>-- <br>David Mobley<br><a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a><br>
949-385-2436<br>
</div></font></span></div>
</blockquote></div><br><br clear="all"><br>-- <br>David Mobley<br><a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a><br>949-385-2436<br>
</div>
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