* Morteza Khabiri <[EMAIL PROTECTED]> [2008-09-09 22:03:36 +0200]:
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.
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
Hello, your faulty itp file results from the string in the second column. It should correspond to the OPLS atom nr, like opls_032. Best Regards, Flo
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 CAKThe 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Florian Dommert Dipl.-Phys. Computational and Theoretical Softmatter & Biophysics group Frankfurt Institute for Advanced Studies Johann-Wolfgang-Goethe University Ruth-Moufang-Str. 1 60438 Frankfurt am Main Phone: +49(0)69 / 798 - 47522 Fax: +49(0)69 / 798 - 47611 EMail: [EMAIL PROTECTED] Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
pgpzCdF6QUenP.pgp
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