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 > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
