[gmx-users] Re: x2top

[程迪]

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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