<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
The best way to find out is by looking at the dihedrals fpor the
aminoacid as defined by the forcefield. Someone may know it by
heart, but to make sure you need to check it yourself anway. It'll
be hard to defend your results before a picky referee by saying that
"this dude on a mailing list said so".<br>
<br>
Erik<br>
<br>
maria goranovic skrev 2011-03-29 11.51:
<blockquote
cite="mid:AANLkTi=d2gWDXFujCzUGztTXc1mm9GrGsuhqiwn5ju=p@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">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 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
moz-do-not-send="true"
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>
<br>
--<br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
</pre>
</body>
</html>