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

Justin A. Lemkul Wed, 13 Jul 2011 08:11:47 -0700


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 thetip3p 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 part of thetop-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-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[ 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
; 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 wheni 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 type resnrresidu 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 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 462750.4 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 O 1108.000 418.400 C C C 1 112.000 488.273H C H 1 109.470 292.000> [ dihedrals ] 1 2 3 4 3 0.41840 1.25520 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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--
========================================

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

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