Thanks Mark,<br><br>1) By the way do you know any database where I could obtain information about function of the specific CAP groups ?<br>E.g as I know the most spread CAP on N is ACE group but in my case there is For ( simple COH group) instead of ACE. <br>
<br>I think that parametrisation of such simple groups should not be very complicate but it's strange that I've not found already built topology for them.<br><br><br>2) Also I've tried to made topology for D amoniacids. I've started with the topology of L analogs e.g for D-val I've created enty based on the Val in .rtp and .hdb files. Not I think I should to invert impropers for the Calpha atoms that new topology represent to true D-isomer :) But I'm not sure about how to make it correctly :)<br>
<br>In .itp I've found for new DVA residue<br><br> [ impropers ]<br>; ai aj ak al gromos type<br> N -C CA H gi_1 <br> CA N C CB gi_2 <br> CA CG1 CG2 CB gi_2 <br>
C CA +N O gi_1 <br><br>here there are 2 enties for the Ca atoms. What should I do with it for invertion?<br><br>James<br> <br><br><div class="gmail_quote">2011/11/10 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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 bgcolor="#FFFFFF" text="#000000"><div class="im">
On 10/11/2011 7:05 PM, James Starlight wrote:
<blockquote 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></div>
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.<div class="im"><br>
<br>
<blockquote type="cite">
<br>
What difference beetwen different caps I cant understand why in my
structure there are so non-standart groups.<br>
</blockquote>
<br></div>
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><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite"><br>
<br>
James<br>
<br>
<div class="gmail_quote">2011/11/9 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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><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 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>
<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 href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>
<div><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>
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Justin A. Lemkul<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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Justin A. Lemkul<br>
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Virginia Tech<br>
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