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On 10/11/2011 7:36 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopxJrYcG=eu6AAPGFYeTTeU-tsSQWkqQVxypVRSWtwybPg@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
People use acetyl rather than formyl cap either because that's what
was used in the experimental system, or because they are simulating
a fragment from a larger peptide and acetyl makes for a better model
of a peptide bond than formyl for only a small extra cost. I don't
even know that any force fields have parameters for H-C(O)-N(H)-R. I
suggest you use acetyl.<br>
<br>
<blockquote
cite="mid:CAALQopxJrYcG=eu6AAPGFYeTTeU-tsSQWkqQVxypVRSWtwybPg@mail.gmail.com"
type="cite"><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>
</blockquote>
<br>
First, identify that there's anything to invert. Look at the #define
lines for gi_1 and gi_2 and the manual sections for impropers.
There's nothing associated with any handedness. The impropers for
chirality prevent inversion, rather than enforcing a particular
chirality. You can test this yourself. Make a .tpr of an L-amino
acid and .gro files of each chirality, and then use mdrun -rerun
Lconfiguration.gro -s Lconfiguration and compare with mdrun -rerun
Rconfiguration.gro -s Lconfiguration.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopxJrYcG=eu6AAPGFYeTTeU-tsSQWkqQVxypVRSWtwybPg@mail.gmail.com"
type="cite"><br>
James<br>
<br>
<br>
<div class="gmail_quote">2011/11/10 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><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 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 moz-do-not-send="true"
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 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> <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><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>
Ph.D. Candidate<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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-- <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>
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