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On 10/11/2011 7:05 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopyyBa8m-GMVY7k8aaa9P0sXp2MEAPu_GkGaeZ+Xi3heng@mail.gmail.com"
type="cite">Justin,<br>
<br>
<br>
I've also look for the cap editing in the pymol but it seems that
that function lacks in that program<br>
<br>
By the way, what are specificity of such Cap groups ? Do they are
only sheld charges on the termi or have something addition
function?<br>
</blockquote>
<br>
They can. The purpose of a simulation is to provide a model of
reality. How one would wish to cap a peptide depends what is being
modelled under what conditions with what objectives in mind.<br>
<br>
<blockquote
cite="mid:CAALQopyyBa8m-GMVY7k8aaa9P0sXp2MEAPu_GkGaeZ+Xi3heng@mail.gmail.com"
type="cite">
<br>
What difference beetwen different caps I cant understand why in my
structure there are so non-standart groups.<br>
</blockquote>
<br>
Shrug. We don't even know what they are... Wherever you sourced your
starting structure should discuss how and why the termini have such
caps.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopyyBa8m-GMVY7k8aaa9P0sXp2MEAPu_GkGaeZ+Xi3heng@mail.gmail.com"
type="cite"><br>
<br>
James<br>
<br>
<div class="gmail_quote">2011/11/9 Justin A. Lemkul <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid
rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left:
1ex;">
<div class="im"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px
solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex;
padding-left: 1ex;">
Justin,<br>
<br>
Could you tell me another alternative ways to replace
existing cap groups in my pdb besides xleap ? ( I've had
many problems with the pdb's processed by this soft).
Also I've tried to make topology for the non-standart caps
by PRODRG but I also have some problems with such
parametrisation.<br>
<br>
</blockquote>
<br>
</div>
Unless you describe your problems, there's very little anyone
can or will try to do to help you. I've never had a problem
with an xleap coordinate file, so I can't offer you any
additional guidance with that. Otherwise, there are dozens of
programs that are capable of drawing molecules or editing
files. See, for instance:<br>
<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources"
target="_blank">http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid
rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left:
1ex;">
<div class="im">
<br>
Also I've not found suitable topology for some D-isomers (
it's strange that parametriation for such typical
non-standart residues is absent in all force fields ). As
I understood I cant use topology of L-analogs for the
parametrisation of such D-forms because I dont know
suitable parameters for dihedrals for instance.<br>
Have someone pre-built parameters for the D-aa for Gromos
or Charmm force field?<br>
<br>
<br>
Thanks,<br>
<br>
James<br>
<br>
</div>
2011/10/29 Justin A. Lemkul <<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>
<div class="im"><br>
<br>
<br>
<br>
James Starlight wrote:<br>
<br>
Justin, hello!<br>
<br>
Could you tell me what exactly program from the
Amber tools<br>
package you've used for the KALP peptide
preparation e.g for<br>
capping ?<br>
<br>
<br>
xleap<br>
<br>
At this point, please start a new thread for your
questions, as<br>
these topics are completely unrelated to where you
started.<br>
<br>
-Justin<br>
<br>
<br>
</div>
-- ==============================__==========
<div class="im"><br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
</div>
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<div>
<div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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