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><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 class="gmail_quote">2011/10/29 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Justin, hello!<br>
<br>
Could you tell me what exactly program from the Amber tools package you've used for the KALP peptide preparation e.g for capping ?<br>
</blockquote>
<br></div>
xleap<br>
<br>
At this point, please start a new thread for your questions, as these topics are completely unrelated to where you started.<br><font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
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==============================<u></u>==========<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 href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
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