Hi, Chaban<br><br>I think the result cannot be trusted because the total charge is 1.2, which seems impossible. I just used the result calculated by Material Studio and I used the value of charge on the internal atoms. The atoms in surface have different charges. I have to change the charge by hand.<br>
<br>P.S. -pbc or -nopbc is depend on if you will use Periodical Boundary Condition. My pdb is a SiO2 sphere, so I used -nopbc<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><br>
<br><br><div class="gmail_quote">On Tue, Mar 23, 2010 at 10:19 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;">
Why the result cannot be trusted? The below warning is always output<br>
by x2top if I'm not mistaken. Anyway, this is a good idea to check the<br>
topologies before starting MD... :)<br>
<br>
P.S. Maybe -nopbc should be used instead - I don't remember exactly.<br>
Use the option which is not default - that is true.<br>
<div><div></div><div class="h5"><br>
<br>
On Tue, Mar 23, 2010 at 3:14 PM, 程迪 <<a href="mailto:chengdi123000@gmail.com">chengdi123000@gmail.com</a>> wrote:<br>
> 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>
><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>
><br>
><br>
><br>
> On Tue, Mar 23, 2010 at 8:10 PM, Vitaly V. Chaban <<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>><br>
> wrote:<br>
>><br>
>> Try to use the following:<br>
>> x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa -pbc<br>
>><br>
>> --<br>
>> Dr. Vitaly Chaban<br>
>> <a href="http://chaban.at.ua" target="_blank">http://chaban.at.ua</a><br>
>><br>
>><br>
>><br>
>><br>
>> ><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<br>
>> > 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<br>
>> > -name<br>
><br>
</div></div></blockquote></div><br>