Res: [gmx-users] Topology for nBuOH
Juliana Angeiras
juangeiras at yahoo.com.br
Wed Jul 13 16:30:10 CEST 2011
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 <jalemkul at vt.edu>
Para: Discussion list for GROMACS users <gmx-users at 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
========================================
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