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

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 26 12:34:41 CEST 2011

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:


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



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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