Hi, really the problem was with the order, but now i have another problem (below). I have already read the chapter 5, but i didn't fix my problem. I would like to use an archive .itp for the butanol, although i use the tip3p for water in the system (mixture water-butanol), I want use different parameters for nonbonded interactions between water-butanol (because were parametrized specifically for these interactions). How can I do that? My atual archive .top is more below.
Archive .top: [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 [ atomtypes ] ; name at.num mass charge ptype V(c6) W(c12) Hb 1 1.0080 0.38 A 0.4149611E-07 0.9737356E-04 O 8 15.9994 -0.66 A 0.9722461E-06 0.1247853E-02 C 6 12.0110 0.40 A 0.4895634E-05 0.2791672E-02 C 6 12.0110 -0.22 A 0.4895634E-05 0.2791672E-02 C 6 12.0110 -0.33 A 0.4895634E-05 0.2791672E-02 H 1 1.0080 -0.06 A 0.4415162E-06 0.5131711E-03 H 1 1.0080 0.11 A 0.4415162E-06 0.5131711E-03 [ bondtype ] ; ai aj funct c0 c1 Hb O 1 0.10900 462750.4 O C 1 0.14300 376560.0 C C 1 0.15300 265265.6 H C 1 0.10800 284512.0 [ angletype ] ; ai aj ak func c0 c1 C O Hb 1 108.000 460.240 C C O 1 108.000 418.400 C C C 1 112.000 488.273 H C H 1 109.470 292.000 [ moleculetype ] ; name nrexcl BuOH 3 [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 Hb 1 BuOH HO 1 0.38 1.0080 2 O 1 BuOH OH 1 -0.66 15.9994 3 C 1 BuOH CA 1 0.40 12.0110 4 C 1 BuOH CB 1 -0.22 12.0110 5 C 1 BuOH CC 1 -0.22 12.0110 6 C 1 BuOH CD 1 -0.33 12.0110 7 H 1 BuOH HA 1 -0.06 1.0080 8 H 1 BuOH Hb 1 -0.06 1.0080 9 H 1 BuOH HC 1 0.11 1.0080 10 H 1 BuOH HD 1 0.11 1.0080 11 H 1 BuOH HE 1 0.11 1.0080 12 H 1 BuOH HF 1 0.11 1.0080 13 H 1 BuOH HG 1 0.11 1.0080 14 H 1 BuOH HF 1 0.11 1.0080 15 H 1 BuOH HG 1 0.11 1.0080 [ dihedrals ] 1 2 3 4 3 0.41840 1.25520 0.00000 -1.67360 0.00000 0.00000 2 3 4 5 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 3 4 5 6 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000 ; Include forcefield parameters ;#include "oplsaa.ff/forcefield.itp" ; Include forcefield parameters #include "oplsaa.ff/tip3p.itp" [ nonbond_params ] ; i j func V(c6) W(c12) H H 1 0.4149611E-07 0.9737356E-04 H HW 1 0.4149611E-07 0.9737356E-04 H C 1 0.4415162E-06 0.5131711E-03 H O 1 0.1927397E-06 0.3416812E-03 H OW 1 0.1927397E-06 0.3416812E-03 H Hb 1 0.4149611E-07 0.9737356E-04 HW HW 1 0.0000000E+00 0.0000000E+00 HW C 1 0.4415162E-06 0.5131711E-03 HW O 1 0.0000000E+00 0.0000000E+00 HW OW 1 0.0000000E+00 0.0000000E+00 HW Hb 1 0.4149611E-07 0.9737356E-04 C C 1 0.4895634E-05 0.2791672E-02 C O 1 0.2159724E-05 0.1866537E-02 C OW 1 0.2159724E-05 0.1866537E-02 C Hb 1 0.4415162E-06 0.5131711E-03 O O 1 0.9722461E-06 0.1247853E-02 O OW 1 0.1562282E-05 0.1785000E-02 O Hb 1 0.0000000E+00 0.0000000E+00 OW OW 1 0.2510400E-05 0.2552000E-02 OW Hb 1 0.0000000E+00 0.0000000E+00 Hb Hb 1 0.4149611E-07 0.9737356E-04 [ system ] ; Name BuOH in water [ molecules ] ; Compound #mols BuOH 343 SOL 185 Error with grompp: WARNING 1 [file BuOHaa.top, line 27]: Overriding atomtype C WARNING 2 [file BuOHaa.top, line 28]: Overriding atomtype C WARNING 3 [file BuOHaa.top, line 30]: Overriding atomtype H ERROR 1 [file BuOHaa.top, line 32]: Invalid directive bondtype WARNING 4 [file BuOHaa.top, line 34]: Too few parameters on line (source file toppush.c, line 246) WARNING 5 [file BuOHaa.top, line 35]: Too few parameters on line (source file toppush.c, line 246) WARNING 6 [file BuOHaa.top, line 36]: Too few parameters on line (source file toppush.c, line 246) WARNING 7 [file BuOHaa.top, line 37]: Too few parameters on line (source file toppush.c, line 246) ERROR 2 [file BuOHaa.top, line 39]: Invalid directive angletype WARNING 8 [file BuOHaa.top, line 41]: Too few parameters on line (source file toppush.c, line 315) WARNING 9 [file BuOHaa.top, line 42]: Too few parameters on line (source file toppush.c, line 315) WARNING 10 [file BuOHaa.top, line 43]: Too few parameters on line (source file toppush.c, line 315) WARNING 11 [file BuOHaa.top, line 44]: Too few parameters on line (source file toppush.c, line 315) Generated 10 of the 10 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 10 of the 10 1-4 parameter combinations ------------------------------------------------------- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1166 Fatal error: Atomtype opls_111 not found Thanks, Juliana Angeiras B. da Silva. Laboratório de Química Teórica e Computacional Departamento de Química Fundamental Universidade Federal de Pernambuco Recife, PE - Brasil. ________________________________ De: Justin A. Lemkul <jalem...@vt.edu> Para: Discussion list for GROMACS users <gmx-users@gromacs.org> Enviadas: Terça-feira, 12 de Julho de 2011 12:42:49 Assunto: Re: [gmx-users] Topology for nBuOH Juliana Angeiras wrote: > Hi, > I'm trying to include parameters of n-butanol in the topology file (below) >(i'm not using opls or other force field for butanol), but when i run the >grompp >program, I obtain the following message: > Fatal error: > Atomtype Hb not found > How can I fix this problem? > Your directives are out of order. If you define new atomtypes, etc. they have to be defined before they can be used. See Chapter 5 of the manual. -Justin > Thanks > Topology file: > ; Include forcefield parameters #include "oplsaa.ff/forcefield.itp" > >; Include forcefield parameters #include "oplsaa.ff/tip5p.itp" [ >moleculetype ] > ; name nrexcl BuOH 3 [ atoms ] ; nr type resnr residu > >atom cgnr charge mass > 1 Hb 1 BuOH HO 1 0.38 1.0080 > 2 O 1 BuOH OH 1 -0.66 15.9994 > 3 C 1 BuOH CA 1 0.40 12.0110 > 4 C 1 BuOH CB 1 -0.22 12.0110 > 5 C 1 BuOH CC 1 -0.22 12.0110 > 6 C 1 BuOH CD 1 -0.33 12.0110 > 7 H 1 BuOH HA 1 -0.06 1.0080 > 8 H 1 BuOH HB 1 -0.06 1.0080 > 9 H 1 BuOH HC 1 0.11 1.0080 > 10 H 1 BuOH HD 1 0.11 1.0080 > 11 H 1 BuOH HE 1 0.11 1.0080 > 12 H 1 BuOH HF 1 0.11 1.0080 > 13 H 1 BuOH HG 1 0.11 1.0080 > 14 H 1 BuOH HF 1 0.11 1.0080 > 15 H 1 BuOH HG 1 0.11 1.0080 > [ atomtypes ] > ; name at.num mass charge ptype V(c6) W(c12) > Hb 1 1.0080 0.38 A 0.4149611E-07 0.9737356E-04 > O 8 15.9994 -0.66 A 0.9722461E-06 0.1247853E-02 > C 6 12.0110 0.40 A 0.4895634E-05 0.2791672E-02 > C 6 12.0110 -0.22 A 0.4895634E-05 0.2791672E-02 C 6 >12.0110 -0.33 A 0.4895634E-05 0.2791672E-02 > H 1 1.0080 -0.06 A 0.4415162E-06 0.5131711E-03 > H 1 1.0080 0.11 A 0.4415162E-06 0.5131711E-03 > [ bondtype ] ; ai aj funct c0 c1 >HB O 1 0.10900 462750.4 O C 1 0.14300 376560.0 >C C 1 0.15300 265265.6 H C 1 0.10800 284512.0 > [ angletype ] ; ai aj ak func c0 c1 >C O HB 1 108.000 460.240 C C O 1 108.000 >418.400 C C C 1 112.000 488.273 H C H 1 > >109.470 292.000 > [ dihedrals ] 1 2 3 4 3 0.41840 1.25520 0.00000 >-1.67360 >0.00000 0.00000 > 2 3 4 5 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000 > 3 4 5 6 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000 > [ nonbond_params ] > ; i j func V(c6) W(c12) > H H 1 0.4149611E-07 0.9737356E-04 > H HW 1 0.4149611E-07 0.9737356E-04 > H C 1 0.4415162E-06 0.5131711E-03 > H O 1 0.1927397E-06 0.3416812E-03 > H OW 1 0.1927397E-06 0.3416812E-03 > H Hb 1 0.4149611E-07 0.9737356E-04 > HW HW 1 0.0000000E+00 0.0000000E+00 > HW C 1 0.4415162E-06 0.5131711E-03 > HW O 1 0.0000000E+00 0.0000000E+00 > HW OW 1 0.0000000E+00 0.0000000E+00 > HW Hb 1 0.4149611E-07 0.9737356E-04 > C C 1 0.4895634E-05 0.2791672E-02 > C O 1 0.2159724E-05 0.1866537E-02 > C OW 1 0.2159724E-05 0.1866537E-02 > C Hb 1 0.4415162E-06 0.5131711E-03 > O O 1 0.9722461E-06 0.1247853E-02 > O OW 1 0.1562282E-05 0.1785000E-02 > O Hb 1 0.0000000E+00 0.0000000E+00 > OW OW 1 0.2510400E-05 0.2552000E-02 > OW Hb 1 0.0000000E+00 0.0000000E+00 > Hb Hb 1 0.4149611E-07 0.9737356E-04 > [ system ] > ; Name > BuOH in water > [ molecules ] > ; Compound #mols > BuOH 343 > SOL 185 > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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