Res: Res: [gmx-users] Topology for nBuOH
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 13 19:04:02 CEST 2011
Juliana Angeiras wrote:
> Hi Justin,
>
> Sorry if I am slow to understand these things, but I really want to use
> gromacs for simulate my system: butanol-water mixture in several
> concentrations, using tip3p for water and include the parameters for
> butanol and for water-butanol intermolecular interactions. Everything I
> tried until now didn't work. First, I did what you suggest: I have
> changed the order for [ nonbond_params ] putting it before the directive
> [ moleculetype ], but the answer of grommp was that HW (tip3p) atom is
> not recognized. Then I have changed the position of the "includes" to
You can't define a molecule before you define the parameters that are to be
applied to it. The force field level must take precedence over the molecule level.
> top of the archive, but the new message of the grompp was that invalid
> order for [ defaults ], that seems obviously for me because is already
> exist in the include archives. Then, I have removed the directive
> defaults, but the new message was that the atomtype order is invalid. My
> question is what is the correct order for these things.
>
The required order of directives is in Table 5.4 (and then 5.5 and 5.6) of the
manual. In your case, you need to have something along the lines of:
#include "oplsaa.ff/forcefield.itp" ; [ defaults ] is here
; After this are your custom entries - note that spelling matters!
; Your previous messages used e.g. "bondtype" and "angletype"
; which are not valid identifiers.
[ atomtypes ]
...
[ bondtypes ]
...
[ angletypes ]
...
[ nonbond_params ]
...
#include "oplsaa.ff/tip3p.itp"
After that list the parameters for n-butanol and finish with [ system ] and [
molecules ] directives to describe the content of the system.
-Justin
> Thanks for your help,
>
> Juliana Angeiras B. da Silva.
> Laboratório de Química Teórica e Computacional
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Recife, PE - Brasil.
>
> The last archive.top:
> ; Include forcefield parameters
> #include "oplsaa.ff/forcefield.itp"
> ; Include forcefield parameters
> #include "oplsaa.ff/tip3p.itp"
>
> ; [ 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
>
> [ 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
>
> [ 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
>
> [ system ]
> ; Name
> BuOH in water
>
> [ molecules ]
> ; Compound #mols
> BuOH 343
> SOL 185
>
> ------------------------------------------------------------------------
> *De:* Justin A. Lemkul <jalemkul at vt.edu>
> *Para:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Enviadas:* Quarta-feira, 13 de Julho de 2011 12:10:03
> *Assunto:* Re: Res: [gmx-users] Topology for nBuOH
>
>
>
> Juliana Angeiras wrote:
> > 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.
> >
>
> Again, your directives are out of order. The [nonbond_params] are part
> of the top-level force field definition and thus must come before the
> molecule definitions.
>
> -Justin
>
> > 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 <mailto:jalemkul at vt.edu>>
> > *Para:* Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto: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
> >
> > ========================================
> > -- gmx-users mailing list gmx-users at gromacs.org
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>
> -- ========================================
>
> 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 at gromacs.org
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--
========================================
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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