<p>Dear all<br>I am using Gromacs 4.5.3 to simulate a system including: CNT+water+surfactant and I want to<br>use opls force field for my whole system.<br>so far I have done following things:<br>1.I copied oplsaa.ff folder in my working directory.<br>
2.I added following lines to atomname2type.n2t<br>C opls_995 0 12.011 1 C 0.142 <br>C opls_996 0 12.011 2 C 0.142 C 0.142 <br>C opls_997 0 12.011 3 C 0.142 C 0.142 C 0.142 <br>
C opls_998 0 12.011 4 C 0.142 C 0.142 C 0.142 C 0.142 <br>3.I added these to ffbonded.itp<br>[ bondtypes ]<br> C C 1 0.14210 478900</p>
<p> [ angletypes ]<br> C C C 1 120.000 397.480</p>
<p>[ dihedraltypes ]<br> C C 1 0.000 167.360 1<br>4.I added these to ffnonbonded.itp<br>opls_995 C 6 12.01100 0.000 A 3.851000e-01 4.39600e-01<br> opls_996 C 6 12.01100 0.000 A 3.851000e-01 4.39600e-01<br>
opls_997 C 6 12.01100 0.000 A 3.851000e-01 4.39600e-01<br> opls_998 C 6 12.01100 0.000 A 3.851000e-01 4.39600e-01<br>5.I used g_x2top to create topology for CNT.<br>Command line was:<br>
g_x2top -f cnt.pdb -o cnt.top -r cnt.rtp -name CNT -nexcl 5 </p>
<p>6.I used TopolGen to produce the *.itp file for surfactant molecule.<br>7.I placed surfactant molecules around CNT.<br>8.I used editconf using this command:<br>editconf -f cnt_sur.pdb -o cnt_sur.gro -c -d 1 -bt cubic<br>
9. I wrote a a .top file given below,<br> Include forcefield parameters<br>#include "./oplsaa.ff/forcefield.itp"<br>; Include topology for DTAB<br>#include "DTAB.itp"<br>; Include topology for CNT<br>
#include "cnt.itp"<br>;<br>[ molecules ]<br>; molecule name nr.<br>DTAB 14<br>CNT 1</p>
<p>10.I called genbox with the command:<br>genbox -cp cnt_sur.gro -cs spc216.gro -p topol.top -o solv.gro<br>11.I added manually these to topol.top<br>; Include SPC water topology<br>#include "oplsaa.ff/spc.itp"</p>
<p>12. once I run grompp : grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr<br>I got following errors:<br>Ignoring obsolete mdp entry 'title'</p>
<p>WARNING 1 [file ffbonded.itp, line 2704]:<br> Overriding Bond parameters.</p>
<p> old: 0.151 292880 0.151 292880 <br> new: C C 1 0.14210 478900</p>
<p>Generated 335790 of the 335790 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 335790 of the 335790 1-4 parameter combinations</p>
<p>ERROR 1 [file DTAB.itp, line 104]:<br> No default Bond types</p>
<p><br>ERROR 2 [file DTAB.itp, line 105]:<br> No default Bond types</p>
<p><br>ERROR 3 [file DTAB.itp, line 241]:<br> No default Angle types</p>
<p><br>ERROR 4 [file DTAB.itp, line 242]:<br> No default Angle types</p>
<p><br>ERROR 5 [file DTAB.itp, line 244]:<br> No default Angle types</p>
<p><br>ERROR 6 [file DTAB.itp, line 245]:<br> No default Angle types</p>
<p><br>ERROR 7 [file DTAB.itp, line 249]:<br> No default Angle types</p>
<p><br>ERROR 8 [file DTAB.itp, line 302]:<br> No default Ryckaert-Bell. types</p>
<p><br>ERROR 9 [file DTAB.itp, line 303]:<br> No default Ryckaert-Bell. types</p>
<p>Excluding 3 bonded neighbours molecule type 'DTAB'<br>Excluding 5 bonded neighbours molecule type 'CNT'<br>Excluding 2 bonded neighbours molecule type 'SOL'</p>
<p>NOTE 1 [file topol.top, line 27]:<br> System has non-zero total charge: 5.039999e+00<br> </p>
<p> </p>
<p>There was 1 note</p>
<p>There was 1 warning</p>
<p>-------------------------------------------------------<br>Program grompp, VERSION 4.5.3<br>Source code file: /build/buildd/gromacs-4.5.3/src/kernel/grompp.c, line: 1356</p>
<div>Fatal error:<br>There were 9 errors in input file(s)<br>-------------------------------------------------------<br>I would be more than pleased if someone could guild me how to solve the problem.</div>
<div> </div>
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