[gmx-users] Re: x2top

[程迪]

Hi, Chaban

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.

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

Di Cheng

University of Science and Technology of China
Hefei, Anhui Province 230026
P. R. China
E-mail: chengdi at mail.ustc.edu.cn
Tel.: +86-15321055911



On Tue, Mar 23, 2010 at 10:19 PM, Vitaly V. Chaban <vvchaban at gmail.com>wrote:

> Why the result cannot be trusted? The below warning is always output
> by x2top if I'm not mistaken. Anyway, this is a good idea to check the
> topologies before starting MD... :)
>
> P.S. Maybe -nopbc should be used instead - I don't remember exactly.
> Use the option which is not default - that is true.
>
>
> On Tue, Mar 23, 2010 at 3:14 PM, 程迪 <chengdi123000 at gmail.com> wrote:
> > Many Thanks to Dr. Vitaly Chaban
> >
> > I just used the command:
> >
> > x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa -nopbc
> >
> > And here's the output
> >
> > ...gromacs' help info...
> > Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> > WARNING: masses will be determined based on residue and atom names,
> >          this can deviate from the real mass of the atom type
> > Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
> > Entries in atommass.dat: 178
> > WARNING: vdwradii will be determined based on residue and atom names,
> >          this can deviate from the real mass of the atom type
> > Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
> > Entries in vdwradii.dat: 28
> > Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
> > Entries in dgsolv.dat: 7
> > Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
> > Entries in electroneg.dat: 71
> > Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
> > Entries in elements.dat: 218
> > Looking whether force field files exist
> > Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp
> > Opening library file ffoplsaa.n2t
> > Opening library file ffoplsaa.n2t
> > There are 6 name to type translations
> > Generating bonds from distances...
> > atom 299
> > There are 2 different atom types in your sample
> > Generating angles and dihedrals from bonds...
> > Before cleaning: 838 pairs
> > Before cleaning: 838 dihedrals
> > There are  312 Ryckaert-Bellemans dihedrals,    0 impropers,  628 angles
> >            838 pairs,      354 bonds and   299 atoms
> > Total charge is 1.2, total mass is 6003.98
> >
> > WARNING: topologies generated by x2top can not be trusted at face value.
> >          Please verify atomtypes and charges by comparison to other
> >          topologies.
> >
> > gcq#309: "Gabba Gabba Hey!" (The Ramones)
> >
> > Seems like it worked :-)
> > But the result cannot be trusted.
> >
> > Di Cheng
> >
> > University of Science and Technology of China
> > Hefei, Anhui Province 230026
> > P. R. China
> > E-mail: chengdi at mail.ustc.edu.cn
> > Tel.: +86-15321055911
> >
> >
> >
> > On Tue, Mar 23, 2010 at 8:10 PM, Vitaly V. Chaban <vvchaban at gmail.com>
> > wrote:
> >>
> >> Try to use the following:
> >> x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa -pbc
> >>
> >> --
> >> Dr. Vitaly Chaban
> >> http://chaban.at.ua
> >>
> >>
> >>
> >>
> >> >
> >> > Hi, everyone
> >> >
> >> > I've just tried x2top.
> >> >
> >> > My ffoplsaa.n2t file is as follows
> >> >
> >> > ;atom   atom_type       charge  mass    neighbor_N      neighbor
> >> > distance
> >> > O       opls_002                -0.3    15.9994 2       SI 0.160 SI
> >> > 0.160
> >> > O       opls_002                -0.3    15.9994 1       SI 0.160
> >> > SI      SI               0.6    28.08   1       O 0.160
> >> > SI      SI               0.6    28.08   2       O 0.160 O 0.160
> >> > SI      SI               0.6    28.08   3       O 0.160 O 0.160 O
> 0.160
> >> > SI      SI               0.6    28.08   4       O 0.160 O 0.160 O
> 0.160
> >> > O
> >> > 0.160
> >> >
> >> > I entered the command below:
> >> >
> >> >  x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa
> >> >
> >> > here's my output:
> >> >
> >> > chengdi at chengdi-desktop:~/Gromacs/sio2$ x2top -f SiO2.pdb -o SiO2.top
> >> > -name
> >
>
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