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: [email protected] Tel.: +86-15321055911 On Tue, Mar 23, 2010 at 10:19 PM, Vitaly V. Chaban <[email protected]>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 <[email protected]> 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: [email protected] > > Tel.: +86-15321055911 > > > > > > > > On Tue, Mar 23, 2010 at 8:10 PM, Vitaly V. Chaban <[email protected]> > > 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: > >> > > >> > chen...@chengdi-desktop:~/Gromacs/sio2$ x2top -f SiO2.pdb -o SiO2.top > >> > -name > > >
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