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>
<br>What difference beetwen different caps I cant understand why in my structure there are so non-standart groups.<br><br><br>James<br><br><div class="gmail_quote">2011/11/9 Justin A. Lemkul <span dir="ltr"><<a 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 href="http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources" target="_blank">http://www.gromacs.org/<u></u>Documentation/File_Formats/<u></u>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 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 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>
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Justin A. Lemkul<br>
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Justin A. Lemkul<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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