[gmx-users] how can I get the .top file??

[Justin A. Lemkul]

Kiwoong Kim wrote:
> Dear members of gromacs
> 
> Let you know that I'm a beginner of Gromacs.
> 
> I am trying to simulate the diffusion problem on some zeolite structure. 
> (especially ZSM-22)
> 
>  >From the manual, I knew that the three files are required to get the 
> .tpr input file.
> I got the .pdb file of my concerned zeolite (zsm-22) but it is 
> impossible to get .top file by using the pdb2gmx because the .pdb file 
> is just coornate file.
> 
> Therefore, my question is how can I get the .top file??
> I already tried the g_x2top -f zeo.pdb -o out.top -ff oplsaa
> but errors were shown
> 
> "Can not find forcefield for atom ~~~~"
> 
> please let me know how to do it....
> 

The force fields in Gromacs are most directly suited to biomolecular systems, so 
their applicability for other materials may be limited.  In any case, the .n2t 
file read by g_x2top is obviously not suited for what you want to do.  You can 
add parameters in the .n2t file, per the following information:

http://www.gromacs.org/Documentation/File_Formats/.n2t_File

Depending on the complexity of the structure, you may or may not be successful.

-Justin

-- 
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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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