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<p class=MsoNormal><span lang=EN-US>Dear Gromacs Users and Developers,<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> </span>│<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> </span>│<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>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>
<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>Department of Biochemistry and Division of
Applied Life Science<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>Gyeonsang National University (GNU)<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>Republic of Korea (South Korea)<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>Email: <a href="mailto:chip@bio.gnu.ac.kr">chip@bio.gnu.ac.kr</a><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>
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