Morteza Khabiri wrote:
Dear
I want to make the solution which is not working with unified atom force
fields. Then I decided to make the itp file by my own.
I made the all atom type ....itp file for opls AA. I found all of the opls
feature in gromacs top directory and according to the top directory files
I made the new itp file. Unfortunately, after running the grompp i faced
with the following error:
Fatal error:
Atomtype 'HC' not found!
but it is defined in the opls.
How so? If you look in ffoplsaa.atp, you will note that all atomtypes are
defined as opls_XXX.
-Justin
My itp file structure is like follow:
;
[ moleculetype ]
; Name nrexcl
DRG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 HC 1 DRG HAD 1 0.02734 1.0080
2 CT 1 DRG CAL 1 0.10638 12.0110
3 HC 1 DRG HAE 1 0.02734 1.0080
4 OS 1 DRG OAI 1 -0.36111 15.9994
5 CT 1 DRG CAK 1 0.10638 12.0110
6 HC 1 DRG HAB 2 0.02734 1.0080
7 HC 1 DRG HAG 2 0.02734 1.0080
8 CY 1 DRG CAM 2 0.00235 12.0110
9 HC 1 DRG HAF 3 0.00857 1.0080
10 HC 1 DRG HAH 3 0.00857 1.0080
11 CY 1 DRG CAJ 3 0.00235 12.0110
12 HC 1 DRG HAC 3 0.00857 1.0080
13 HC 1 DRG HAA 3 0.00857 1.0080
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.109 284512.0 0.109 284512.0 ; HAD CAL
2 3 1 0.109 284512.0 0.109 284512.0 ; CAL HAE
2 4 1 0.141 267776.0 0.141 267776.0 ; CAL HAI
2 11 1 0.152 217568.0 0.152 217568.0 ; CAL CAJ
4 5 1 0.141 267776.0 0.141 267776.0 ; OAI CAK
5 6 1 0.109 284512.0 0.109 284512.0 ; CAK HAB
5 7 1 0.109 284512.0 0.109 284512.0 ; CAK HAG
5 8 1 0.151 234304.0 0.151 234304.0 ; CAK CAM
8 9 1 0.108 284512.0 0.108 284512.0 ; CAM HAF
8 10 1 0.108 284512.0 0.108 284512.0 ; CAM HAH
8 11 1 0.150 217568.0 0.150 217568.0 ; CAM CAJ
11 12 1 0.108 284512.0 0.108 284512.0 ; CAJ HAC
11 13 1 0.108 284512.0 0.108 284512.0 ; CAJ HAA
[ pairs ]
; ai aj fu c0, c1, ...
1 5 1 ; HAD CAK
1 8 1 ; HAD CAM
1 12 1 ; HAD HAC
1 13 1 ; HAD HAA
2 6 1 ; CAL HAB
2 7 1 ; CAL HAG
2 9 1 ; CAL HAF
2 10 1 ; CAL HAH
3 5 1 ; HAE CAK
3 8 1 ; HAE CAM
3 12 1 ; HAE HAC
6 9 1 ; HAB HAF
8 10 1 ; HAB HAH
6 11 1 ; HAB CAJ
7 9 1 ; HAG HAF
7 10 1 ; HAG HAH
7 11 1 ; HAG CAJ
9 12 1 ; HAF HAC
9 13 1 ; HAF HAA
10 12 1 ; HAH HAC
10 13 1 ; HAH HAA
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 107.8 276.1 107.8 276.1 ; HAD CAL HAE
1 2 4 1 109.5 292.8 109.5 292.8 ; HAD CAL OAI
1 2 11 1 110.7 313.8 109.5 397.5 ; HAD CAL CAJ
3 2 4 1 109.5 292.8 109.5 292.8 ; HAE CAL OAI
3 2 11 1 110.7 313.8 110.7 313.8 ; HAE CAL CAJ
4 2 11 1 109.5 292.8 109.5 292.8 ; OAI CAL CAJ
2 4 5 1 109.5 502.0 109.5 502.0 ; CAL OAI CAK
4 5 6 1 109.5 292.8 109.5 292.8 ; OAI CAK HAB
4 5 7 1 109.5 292.8 109.5 292.8 ; OAI CAK HAG
4 5 8 1 109.5 292.8 109.5 292.8 ; OAI CAK CAM
6 5 7 1 107.8 276.1 107.8 276.1 ; HAB CAK HAG
6 5 8 1 110.7 313.8 110.7 313.8 ; HAB CAK CAM
7 5 8 1 110.7 313.8 110.7 313.8 ; HAG CAK CAM
5 8 9 1 114.3 292.8 114.3 292.8 ; CAK CAM HAF
5 8 10 1 114.3 292.8 114.3 292.8 ; CAK CAM HAH
5 8 11 1 117.2 313.8 117.2 313.8 ; CAK CAM CAJ
9 8 10 1 114.3 292.8 114.3 292.8 ; HAF CAM HAH
9 8 11 1 117.2 313.8 117.2 313.8 ; HAF CAM CAJ
10 8 11 1 117.2 313.8 117.2 313.8 ; HAH CAM CAJ
2 11 8 1 117.2 313.8 117.2 313.8 ; CAL CAJ CAM
2 11 12 1 114.3 292.8 114.3 292.8 ; CAL CAJ HAC
2 11 13 1 114.3 292.8 114.3 292.8 ; CAL CAJ HAA
8 11 12 1 117.2 313.8 117.2 313.8 ; CAM CAJ HAC
8 11 13 1 117.2 313.8 117.2 313.8 ; CAM CAJ HAA
12 11 13 1 114.3 292.8 114.3 292.8 ; HAC CAJ HAA
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 1 3 4 3 1.58 4.769 1.58 4.769 ; imp CAL HAD
HAE OAI
5 4 6 7 3 1.58 4.769 1.58 4.769 ; imp CAK OAI
HAB HAG
8 5 10 9 3 0.62 1.882 0.62 1.882 ; imp CAM CAK
HAH HAF
11 2 12 8 3 0.62 1.882 0.62 1.882 ; imp CAJ CAL
HAC CAM
1 2 4 5 3 1.5 4.7 3 1.5 4.7 3 ; dih HAD CAL
OAI CAK
13 11 2 1 3 1.5 4.7 3 1.5 4.7 3 ; dih HAA CAJ
CAL HAD
2 4 5 8 3 1.5 4.7 3 1.5 4.7 3 ; dih CAL OAI
CAK CAM
11 8 5 4 3 1.5 4.7 3 1.5 4.7 3 ; dih CAJ CAM
CAK OAI
13 11 8 5 3 0.6 1.8 3 0.6 1.8 3 ; dih HAA CAJ
CAM CAK
The top file is also set to OPLS forcefield.
I don't know what is wrong exactly. Thats very nice of you if you could
help me.
Thank you very much in advance
Morteza
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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