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

Kiwoong Kim kimkw at sogang.ac.kr
Wed Oct 26 09:36:15 CEST 2011

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....


Kiwoong, Kim.
No. 409/Ricci Hall/Dept. of Chemical & Biomolecular Engineering/
Sogang University/Sinsoo-Dong/Mapo-Gu/Seoul 121-742/ Korea
(office) +82-2-705-8477
(CP) +82-10-8714-2208
(fax) +82-2-3272-0319
(E-mail) kimkw at sogang.ac.kr

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111026/cf7405ad/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: kimkw at sogang.ac.kr.gif
Type: image/gif
Size: 44 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111026/cf7405ad/attachment.gif>

More information about the gromacs.org_gmx-users mailing list