Many Thanks to Dr. Vitaly Chaban<br><br>I just used the command:<br><br>x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa -nopbc<br><br>And here's the output <br><br>...gromacs' help info...<br>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>
WARNING: masses will be determined based on residue and atom names,<br> this can deviate from the real mass of the atom type<br>Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat<br>Entries in atommass.dat: 178<br>
WARNING: vdwradii will be determined based on residue and atom names,<br> this can deviate from the real mass of the atom type<br>Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat<br>Entries in vdwradii.dat: 28<br>
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat<br>Entries in dgsolv.dat: 7<br>Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat<br>Entries in electroneg.dat: 71<br>Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat<br>
Entries in elements.dat: 218<br>Looking whether force field files exist<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp<br>Opening library file ffoplsaa.n2t<br>Opening library file ffoplsaa.n2t<br>
There are 6 name to type translations<br>Generating bonds from distances...<br>atom 299<br>There are 2 different atom types in your sample<br>Generating angles and dihedrals from bonds...<br>Before cleaning: 838 pairs<br>
Before cleaning: 838 dihedrals<br>There are 312 Ryckaert-Bellemans dihedrals, 0 impropers, 628 angles<br> 838 pairs, 354 bonds and 299 atoms<br>Total charge is 1.2, total mass is 6003.98<br><br>WARNING: topologies generated by x2top can not be trusted at face value.<br>
Please verify atomtypes and charges by comparison to other<br> topologies.<br><br>gcq#309: "Gabba Gabba Hey!" (The Ramones)<br><br>Seems like it worked :-)<br>But the result cannot be trusted.<br clear="all">
<br>Di Cheng<br><br>University of Science and Technology of China<br>Hefei, Anhui Province 230026<br>P. R. China<br>E-mail: <a href="mailto:chengdi@mail.ustc.edu.cn">chengdi@mail.ustc.edu.cn</a><br>Tel.: +86-15321055911<br>
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<br><br><div class="gmail_quote">On Tue, Mar 23, 2010 at 8:10 PM, Vitaly V. Chaban <span dir="ltr"><<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Try to use the following:<br>
x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa -pbc<br>
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--<br>
Dr. Vitaly Chaban<br>
<a href="http://chaban.at.ua" target="_blank">http://chaban.at.ua</a><br>
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><br>
> Hi, everyone<br>
><br>
> I've just tried x2top.<br>
><br>
> My ffoplsaa.n2t file is as follows<br>
><br>
> ;atom atom_type charge mass neighbor_N neighbor<br>
> distance<br>
> O opls_002 -0.3 15.9994 2 SI 0.160 SI<br>
> 0.160<br>
> O opls_002 -0.3 15.9994 1 SI 0.160<br>
> SI SI 0.6 28.08 1 O 0.160<br>
> SI SI 0.6 28.08 2 O 0.160 O 0.160<br>
> SI SI 0.6 28.08 3 O 0.160 O 0.160 O 0.160<br>
> SI SI 0.6 28.08 4 O 0.160 O 0.160 O 0.160 O<br>
> 0.160<br>
><br>
> I entered the command below:<br>
><br>
> x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa<br>
><br>
> here's my output:<br>
><br>
> chengdi@chengdi-desktop:~/Gromacs/sio2$ x2top -f SiO2.pdb -o SiO2.top -name<br>
</blockquote></div><br>