[gmx-users] on x2top, Need for help!

[徐志平]

Dear all:
     I am trying to run MD simulations on carbon nanotube, so I generate
my coordinate file as:

CNT.pdb
--------------------------------------------------------
Carbon Nanotube
600
    1CNT  CB  1    0.274  0.199  -1.167  
.......
    40 23.15 40
--------------------------------------------------------
     then I run 
          >x2top -f CNT.pdb -o CNT.top -r CNT.rtp
          with a selection on 0: Gromacs forcefield.
     but it reports an error as "no forcefield type for atom CB(1) with
2 bonds", so I check the previous posts, someone suggested to have a
modification on ffgmx.n2t.
     so I add some lines below  "CB  CB  3  CB  CB  CB", but  I am not
sure because I am not familiar with those files.
--------------------------------------------------------
CB  CB  3  CB   CB      CB
CB  CB  2  CB   CB
--------------------------------------------------------
       then it works well, furthmore I'd like to use periodic boudary
condition, and run 
          >export GMXFULLPBC=1
          >x2top -f CNT.pdb -o CNT.top -r CNT.rtp -pbc
          But it does not work, the atoms near one boundary are not
bonded with those near the oppsite one, I do not know if x2top read PBC
from the last line of *gro file.
          Can anyone help me? Thanks a lot.


Best Regards.

ZP

-----------------------------------------------
徐 志平 / Xu ZhiPing
Ph.D Candidate
Room: 3405, Phone: 86-10-627-83814
Department of Mechanics,
Qinghua University, Beijing, CHINA
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