Just curious, this would also hold true for the OPLA-AA force field. It is all-atom, so no changes seems to be necessary besides making a d-amino acid in the input ? <br><br><div class="gmail_quote">On Mon, Mar 28, 2011 at 2:13 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 28/03/2011 8:45 PM, maria goranovic wrote:
<blockquote type="cite">That would mean that a new residue type will not be
required? I just need the correct input D-coordinates? <br>
</blockquote>
<br></div>
Try it, before asking about it :-) I said "I suspect you do not need
to change anything about the topology", but I haven't actually done
anything like this ever. Topologies and code shouldn't care about
chirality, so you shouldn't need to do anything other than input the
configuration you want.<br><font color="#888888">
<br>
Mark</font><div class="im"><br>
<br>
<blockquote type="cite">
<div class="gmail_quote">On Sat, Mar 26, 2011 at 2:02 AM, Mark
Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
<div text="#000000" bgcolor="#ffffff">
<div> On 26/03/2011 2:27 AM, maria goranovic
wrote:
<blockquote type="cite">Yes, that would be the correct way
to do this. I was hoping to take a shorter route, and
just modifying a couple of dihedrals in the topology
files output by pdb2gmx without having to make a new
residue. Is that not possible at all ?</blockquote>
<br>
</div>
Unlike (say) AMBER's leap, pdb2gmx doesn't generate
coordinates in a general sense. It generates a topology that
matches given coordinates, fixing a few details as directed.
It will fill valences with hydrogen atoms, generate terminal
groups, organize disulfides, and choose protonation states
of titratable residues, but it won't change geometries in
the way you seem to want.<br>
<br>
Neither does anything in the .top/.itp files stipulate the
chirality of any center (in all-atom models). Various
dihedral angles change sign with chirality, but the dihedral
functions are all symmetric about the y-axis (i.e. even). So
I suspect you do not need to change anything about the
topology. Just use a molecule builder to change the
chirality of the relevant center in the input file to
pdb2gmx.<br>
<font color="#888888"> <br>
Mark</font><br>
</div>
</blockquote>
</div>
</blockquote>
<br>
</div></div>
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