[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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