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<body lang="KO" link="blue" vlink="purple">you will have to find the parameters for a carbocation in this configuration from someone who has derived them before, if acpype doesn't know about the species in this configuration, or derive them yourself using ab initio/semiempiracle methods (i.e. gaussian). Also remember you'll need angle and dihedral parameters too (so the pairwise vdw coefficients is not your only problem).<br>
-- <br>
Sent from my Android phone with K-9 Mail. Please excuse my brevity.<br><br><div class="gmail_quote">chip <chip@bio.gnu.ac.kr> wrote:<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="Section1">
<p class="MsoNormal"><span lang="EN-US">Please anybody help me<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I'm trying to simulate a protein-ligand
complex system using GROMACS 4.5.3 and Amber03 forcefield.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">In this system, a carbocationic
intermediate was used as ligand<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">C - C+ - C - C - O-PP (Carbocationic
intermediate)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> │<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> C<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I tried to obtain topology file for
intermediate molecule using ACPYPE<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">[Command: acpype -i intermediate.mol2 -n
-2]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">But, ACPYPE didn't recognize the
carbocation<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">So, I firstly obtained topology file for
substrate molecule<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">C = C - C - C - O-PP (Substrate: IPP)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> │<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> C<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">[Command: acpype -i IPP.mol2 -n -3]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Then, I tried to modify [atomtypes] in
IPP.itp file by adding atomtype for carbocationic carbon<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">But, I couldn't do this<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">[ atomtypes ] <--- IPP.itp
=================================================================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">;name
bond_type mass
charge ptype sigma
epsilon Amb<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> c3
c3 0.00000
0.00000 A 3.39967e-01
4.57730e-01 ; 1.91 0.1094 ; single bonded carbon<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> c2
c2 0.00000
0.00000 A 3.39967e-01
3.59824e-01 ; 1.91 0.0860 ; double bonded carbon<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> os
os 0.00000
0.00000 A 3.00001e-01
7.11280e-01 ; 1.68 0.1700<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> p5
p5 0.00000
0.00000 A 3.74177e-01
8.36800e-01 ; 2.10 0.2000<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> o
o 0.00000
0.00000 A 2.95992e-01
8.78640e-01 ; 1.66 0.2100<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> h1
h1 0.00000
0.00000 A 2.47135e-01
6.56888e-02 ; 1.39 0.0157<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> hc
hc 0.00000
0.00000 A 2.64953e-01
6.56888e-02 ; 1.49 0.0157<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> ha
ha 0.00000
0.00000 A 2.59964e-01
6.27600e-02 ; 1.46 0.0150<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">=============================================================================================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">how to obtain sigma and epsilon values for
carbocationinc carbon ?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I've read the manual, but I'm still none
the wiser<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I'am a lack of knowledge about this<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Please kindly give some suggestions and
comments <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Is it right this way to make the topology
file for carbocationic intermediate ?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Chanin Park<o:p></o:p></span></p>
</div>
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