程迪 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.
Any parameters assigned (by any method, automated or otherwise) must be
validated in the context of the force field chosen. The warning is mostly there
to prevent unsuspecting users from plowing forward with lots of work without
realizing the nuances of deriving suitable parameters.
-Justin
Di Cheng
University of Science and Technology of China
Hefei, Anhui Province 230026
P. R. China
E-mail: [email protected] <mailto:[email protected]>
Tel.: +86-15321055911
On Tue, Mar 23, 2010 at 8:10 PM, Vitaly V. Chaban <[email protected]
<mailto:[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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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