[gmx-users] X2top error, Could only find a forcefield type for 0 out of 66 atoms

John Adams john.adams1395 at gmail.com
Wed Mar 7 19:47:56 CET 2018


Dear Gromacs users,
I am trying to transform my PDP file for AL2O3 surface to a top file using
x2top. I have defined my forcefield.itp and .n2t file. However, I keep
recieving an error telling me that "Could only find a forcefield type for 0
out of 66 atoms"

my PDB file looks like
COMPND    UNNAMED
AUTHOR    GENERATED BY OPEN BABEL 2.3.2
CRYST1    4.759    8.243   17.151  90.00  90.00  90.00 P1          1
HETATM    1  O   LIG     1       3.201   0.667   3.490  1.00  0.00
  O
HETATM    2  O   LIG     1       0.822   4.789   3.490  1.00  0.00
  O
HETATM    3  O   LIG     1       0.822   2.041   7.821  1.00  0.00
  O
HETATM    4  O   LIG     1       3.201   6.163   7.821  1.00  0.00
  O
HETATM    5  B   LIG     1       3.201   3.415  12.151  1.00  0.00
  B
HETATM    6  B   LIG     2       0.822   7.536  12.151  1.00  0.00
  B
HETATM    7  O   LIG     1       1.017   1.928   3.490  1.00  0.00
  O
HETATM    8  O   LIG     1       3.397   6.050   3.490  1.00  0.00
  O
HETATM    9  O   LIG     1       3.397   3.302   7.821  1.00  0.00
  O
HETATM   10  O   LIG     1       1.017   7.424   7.821  1.00  0.00
  O


my itp file looks like
 #define _ff_clayff
 [ defaults ]
   ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
   1               2               yes             0.5     0.5

[ atomtypes ]

; name       mass      charge    ptype      sigma      eps
 ho   1      1.00800     0.4250    A    0.00000e-01  0.00000e-01
;clayFF_hydroxylhydrogen
 oh   8     15.99800    -0.9500    A    3.16557e-01  6.50209e-01
;ClayFF_hydroxyloxygen
 ob   8     15.99800    -1.0500    A    3.16557e-01  6.50209e-01
;ClayFF_bridgingoxyge
 ao  13     26.98200     1.5750    A    4.27128e-01  6.0e-06
;ClayFF_octahedalaluminium

[ bondtypes ]
; i    j  func       b0          kb
   oh     ho   1        0.1000     554134.9

 [ angletypes ]
 ;  i    j    k  func       th0       cth
   ao   oh    ho    1        109.47    125.52


my .n2t file looks like

B   oh   -0.9500    15.998  1    H   0.100              ;hydroxyl oxygen
O   ob   -1.2996    15.998  0                           ;bridging oxygen
with double substitution
H   ho   -1.0808    15.998  1    B   0.100              ;hydroxyl hydrogen
with substitution
AL  ao    1.5750    26.982  0                           ;octahedral
aluminium


Your help is really appreciated
Regards


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