[gmx-users] Re: x2top

[Justin A. Lemkul]

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: chengdi at mail.ustc.edu.cn <mailto: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 
> <mailto: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
> 
> 

-- 
========================================

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

========================================