Re: Res: Res: [gmx-users] Topology for nBuOH

Justin A. Lemkul Wed, 13 Jul 2011 10:06:25 -0700


Juliana Angeiras wrote:

Hi Justin,
Sorry if I am slow to understand these things, but I really want to usegromacs for simulate my system: butanol-water mixture in severalconcentrations, using tip3p for water and include the parameters forbutanol and for water-butanol intermolecular interactions. Everything Itried until now didn't work. First, I did what you suggest: I havechanged the order for [ nonbond_params ] putting it before the directive[ moleculetype ], but the answer of grommp was that HW (tip3p) atom isnot 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 beapplied 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 invalidorder for [ defaults ], that seems obviously for me because is alreadyexist in the include archives. Then, I have removed the directivedefaults, but the new message was that the atomtype order is invalid. Myquestion 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 themanual. 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-02C 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 c1Hb O 1 0.10900 462750.4O C 1 0.14300 376560.0C C 1 0.15300 265265.6H C 1 0.10800 284512.0[ angletype ]; ai aj ak func c0 c1C O Hb 1 108.000 460.240C C O 1 108.000 418.400C C C 1 112.000 488.273H 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 nrexclBuOH 3[ atoms ]; nr type resnr residu atom cgnr charge mass1 Hb 1 BuOH HO 1 0.38 1.00802 O 1 BuOH OH 1 -0.66 15.99943 C 1 BuOH CA 1 0.40 12.01104 C 1 BuOH CB 1 -0.22 12.01105 C 1 BuOH CC 1 -0.22 12.01106 C 1 BuOH CD 1 -0.33 12.01107 H 1 BuOH HA 1 -0.06 1.00808 H 1 BuOH Hb 1 -0.06 1.00809 H 1 BuOH HC 1 0.11 1.008010 H 1 BuOH HD 1 0.11 1.008011 H 1 BuOH HE 1 0.11 1.008012 H 1 BuOH HF 1 0.11 1.008013 H 1 BuOH HG 1 0.11 1.008014 H 1 BuOH HF 1 0.11 1.008015 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 <[email protected]>
*Para:* Discussion list for GROMACS users <[email protected]>
*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 anotherproblem (below). I have already read the chapter 5, but i didn't fix myproblem. I would like to use an archive .itp for the butanol, although iuse the tip3p for water in the system (mixture water-butanol), I wantuse different parameters for nonbonded interactions betweenwater-butanol (because were parametrized specifically for theseinteractions). How can I do that? My atual archive .top is more below.>Again, your directives are out of order. The [nonbond_params] are partof the top-level force field definition and thus must come before themolecule 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 612.0110 -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 c1Hb O 1 0.10900 462750.4O C 1 0.14300 376560.0C C 1 0.15300 265265.6H C 1 0.10800 284512.0> [ angletype ]; ai aj ak func c0 c1C O Hb 1 108.000 460.240C C O 1 108.000 418.400C C C 1 112.000 488.273H C H 1 109.470 292.000> [ moleculetype ]; name nrexclBuOH 3[ atoms ]; nr type resnr residu atom cgnr charge mass> 1 Hb 1 BuOH HO 1 0.38 1.00802 O 1 BuOH OH 1 -0.66 15.9994 3C 1 BuOH CA 1 0.40 12.0110 4C 1 BuOH CB 1 -0.22 12.0110 5 C1 BuOH CC 1 -0.22 12.0110 6 C 1BuOH CD 1 -0.33 12.0110 7 H 1BuOH HA 1 -0.06 1.0080 8 H 1 BuOHHb 1 -0.06 1.0080 9 H 1 BuOH HC1 0.11 1.0080 10 H 1 BuOH HD 10.11 1.0080 11 H 1 BuOH HE 1 0.111.0080 12 H 1 BuOH HF 1 0.111.0080 13 H 1 BuOH HG 1 0.11 1.008014 H 1 BuOH HF 1 0.11 1.008015 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 <[email protected] <mailto:[email protected]>>
> *Para:* Discussion list for GROMACS users <[email protected]<mailto:[email protected]>>
 > *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 topologyfile (below) (i'm not using opls or other force field for butanol), butwhen 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 themanual.
 >
 > -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 typeresnr 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 C6 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 c0c1 HB O 1 0.10900 462750.4 O C 1 0.14300376560.0 C C 1 0.15300 265265.6 H C 10.10800 284512.0> > [ angletype ] ; ai aj ak func c0c1 C O HB 1 108.000 460.240 C C O1 108.000 418.400 C C C 1 112.000 488.273H C H 1 109.470 292.000> > [ dihedrals ] 1 2 3 4 3 0.41840 1.255200.00000 -1.67360 0.00000 0.00000> > 2 3 4 5 3 2.87441 0.58158 2.09200 -5.54799 0.000000.00000> > 3 4 5 6 3 2.92880 -1.46440 0.20920 -1.67360 0.000000.00000
 >  >  [ 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 [email protected]<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>>
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive athttp://www.gromacs.org/Support/Mailing_Lists/Search before posting!> Please don't post (un)subscribe requests to the list. Use the wwwinterface or send it to [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>.
 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- ========================================

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 [email protected]<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive athttp://www.gromacs.org/Support/Mailing_Lists/Search before posting!Please don't post (un)subscribe requests to the list. Use the wwwinterface or send it to [email protected]<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


--
========================================

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    [email protected]
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 thewww interface or send it to [email protected].

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: Res: Res: [gmx-users] Topology for nBuOH

Reply via email to