"No default Angle types" even if angletypes is defined in .top

User discussions
1

Hi,

I am trying to create my own topology to simulate a slab of amorphous silica. Since it involves a blend of custom atomtypes on one hand and some parameters taken from CHARMM on the other, I though the only way to go was to copy-paste the lines I needed from the files in charmm27.ff. Even if I add both bondtypes and angletypes (I have no dihedrals), I still get the error “No default Angle types” when running gmx grompp. Can someone tell me what’s wrong with my topology file? Is it the order of directives? I am sorry, I am not really accustomed to making this kind of ‘makeshift’ topologies.

[ defaults ]
; nbfunc        comb-rule       gen-pairs
;           1: Geometric (one parameter)
;           2: Lorentz-Berthelot
;           3: Geometric (both parameters)
1               2               yes

[ atomtypes ]
; name  at.num   mass     charge  ptype    sigma       epsilon
; Silicon atom for the substrate or dandling
SIP      14       28.0855    0    A        0.3826      1.2552
; Oxygen atom for the substrate
OS	 8        9.95140    0    A        0.3118      0.6276
; Oxygen atom dandling
DO	 8        9.95140    0    A        0.3118      1.2552
; Silanol groups
CT2	6	12.01100	-0.18	A	0.387540942391	0.23012
OH1	8	15.999400	-0.54	A	0.315378146222	0.6363864
H	1	1.008000	0.31	A	0.0400013524445	0.192464 

[ bondtypes ]
OH1	CT2	1	0.142	358150.4
OH1	H	1	0.096	456056.0

[ angletypes ]
H	OH1	CT2	5	106.0000	481.16	0.0	0.0

[ moleculetype ]
; Name        nrexcl
SRS           3
[ atoms ]
; id  attype resnr  residue  atname  cgnr   charge      mass
  1   SIP     1     SRS      RS      1      0.9
[ position_restraints ]
  1  1  10000 10000 10000

[ moleculetype ]
; Name        nrexcl
SRO           3
[ atoms ]
; id  attype resnr  residue  atname  cgnr   charge      mass
  1   OS     1      SRO      RO      1      -0.45
[ position_restraints ]
  1  1  10000 10000 10000

[ moleculetype ]
; Name        nrexcl
DAO           3
[ atoms ]
; id  attype resnr  residue  atname  cgnr   charge      mass
  1   DO     1      DAO      DO      1      -0.45
[ position_restraints ]
  1  1  10000 10000 10000

[ moleculetype ]
; Name        nrexcl
SBS           3
[ atoms ]
; id  attype resnr  residue  atname  cgnr   charge      mass
  1   SIP    1      SBS      BS      1      0.9
[ position_restraints ]
  1  1  10000 10000 10000

[ moleculetype ]
; Name        nrexcl
SBO           3
[ atoms ]
; id  attype resnr  residue  atname  cgnr   charge      mass
  1   OS     1      SBO      BO      1      -0.42536589516678014
[ position_restraints ]
  1  1  10000 10000 10000

; Silanol groups
[ moleculetype ]
; Name        nrexcl
SIL           3
[ atoms ]
; id  attype resnr  residue  atname  cgnr   charge      mass
  1   CT2     1      SIL      Si      1     -0.18       
  2   OH1     1      SIL      O       1     -0.54       
  3   H       1      SIL      H       1      0.31       
[ bonds ]
;  ai    aj funct
    1     2     1
    2     3     1
[ angles ]
;  	ai    	aj    	ak	funct
	1	2	3	1
[ position_restraints ]
  1  1  10000 10000 10000

[ system ]
AmorphousSilica

[ molecules ]
SRS 2808
SRO 5554
DAO 288
SBS 2938
SBO 5876
SIL 105
2

You are specifying function type 1 (harmonic) in the [moleculetype] definition but the parameters you supply in [angletypes] are function type 5 (Urey-Bradley), so grompp reports that it cannot find matching parameters since you haven’t defined any that are simple harmonic. Changing the function type to 5 in the [moleculetype] definition should solve this issue.

1 Like
3

Ok, funct has to match. Thank you!

4

excuse me, can you explain detaily for me how to Changing the function type? I am a beginer and i am facing with the same error when i work with complex of protein-dna.

5

Hi! In my case I had for atomtypes CT2, OH1 and H:

...
[ angletypes ]
H	OH1	CT2	5	106.0000	481.16	0.0	0.0
...

and molecule definition:

; Silanol groups
[ moleculetype ]
; Name        nrexcl
SIL           3
[ atoms ]
; id  attype resnr  residue  atname  cgnr   charge      mass
  1   CT2     1      SIL      Si      1     -0.18       
  2   OH1     1      SIL      O       1     -0.54       
  3   H       1      SIL      H       1      0.31     
...
[ angles ]
;  	ai    	aj    	ak	funct
	1	2	3	1
...

So I just changed the angle directive in the molecule definition to:

[ angles ]
;  	ai    	aj    	ak	funct
	1	2	3	5
6

image
image1034×416 12.8 KB

I have changed like your recommendation but it is still error :< The error was presented like picture

7

Does it occur at the same line of the topology file?

8

No, at 2 different lines.