[gmx-users] Re: x2top

[Vitaly V. Chaban]

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
>