[gmx-users] CNT (.top) and (.gro) files

Dr. Ramón Garduño-Juárez ramon at fis.unam.mx
Thu Mar 18 02:03:01 CET 2004

  Dear gmx users:

  I am really stuck in my project. I am modeling a carbon nanotube - protein system and I can not figure out how to set the topology files for the CNT (carbon nanotube). All I have is a PDB like file for the CNT and for the protein.

  By reading past messages on the GMX discussion list it seems that I have to include some extra information in the ffgmx.* files, particularly the ffgmx.n2t file but in order to do this I need to know the meaning of the fields of this file which I copy below.

  I will appreciate very much if anyone can shine some light into my darkness.

  Much obliged,


  O    O       1     C                              ; CARBONYL OXYGEN (C=O)
  O    OM    1     C                              ; CARBOXYL OXYGEN (CO-)
  O    OA     2     C    H                       ; HYDROXYL OXYGEN (OH)
  O    OW    2     H    H                       ; WATER OXYGEN
  N     N       3      H    C     C               ; PEPTIDE NITROGEN (N OR NH)
  N     NT     3     H     H     C              ; TERMINAL NITROGEN (NH2)
  N     NL     4     C     H     H     H       ; TERMINAL NITROGEN (NH3)
  N     NR5   2     C     C                      ; AROMATIC N (5-RING,2 BONDS)
  N     NR5*  3     C     C     H              ; AROMATIC N (5-RING,3 BONDS)
  N     NP     3     C     C     FE            ; PORPHYRIN NITROGEN
  C     C       3     C     O      *              ; BARE CARBON (PEPTIDE,C=O,C-N)
  ; Note that order is importante here because of wildcards.
  C     C3     4      H     H     H     *        ; ALIPHATIC CH3 GROUP
  C     C2     4      H     H     C     *        ; ALIPHATIC CH2 GROUP
  C     C1     4      H     C      *     *         ; ALIPHATIC CH GROUP
  C     CB     3      C     C     C               ; BARE CARBON (5-,6-RING)
  H     H       1      N                              ; HYDROGEN BONDED TO NITROGEN
  H     HO     1      O                             ; HYDROXYL HYDROGEN
  H     HW    1      OW                          ; WATER HYDROGEN
  H     HS     1      S                             ; HYDROGEN BONDED TO SULFUR 
  H     HC     1      C                             ; HYDROGEN BONDED TO CARBON

  Dr. Ramón Garduño-Juárez
  Centro de Ciencias Físicas, UNAM
  Phone (777)3291749, (55)56227749
  FAX (777)3291775, (55)56227775
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