[gmx-users] topology file for methane.

[Justin A. Lemkul]

xianghong qi wrote:
> Hi, Justin:
> I am reading chapter 5 now. Still feel confused. I wrote methane.top 
> file like this:
> 
> ; Methane topology file
> ;
> ; The force field files to be included
> #include "ffoplsaa.itp"
> 
> [ moleculetype ]
> ; Name            nrexcl
>  METH             3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> typeB    chargeB      massB
>      1   opls_138      1    METH     C      1      -0.24     12.011   ; 
> qtot 0.61
>      2   opls_140      1    METH     H      1       0.06      1.008   ; 
> qtot 0.67
>      3   opls_140      1    METH     H      1       0.06      1.008   ; 
> qtot 0.67
>      4   opls_140      1    METH     H      1       0.06      1.008   ; 
> qtot 0.73
>      5   opls_140      1    METH     H      1       0.06      1.008   ; 
> qtot 0.79
> 
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     1
>     1     3     1
>     1     4     1
>     1     5     1
> 
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> 
> ; Include water topology
> #include "spc.itp"
> 
> [ system ]
> ; Name
> Methane
> 
> [ molecules ]
> ; Compound        #mols
> METH             1
> ; ;;;;;;;
> 
> Then I should go to ffoplsaa.rtp file to add a new molecule like :
> 
> [METH]
>  [ atoms ]
>      C    opls_135   -0.240     1
>    HC1    opls_140    0.060     1
>    HC2    opls_140    0.060     1
>    HC3    opls_140    0.060     1
>    HC4    opls_140    0.60      1
>  [ bonds ]
>      C  HC1
>      C  HC2
>      C  HC3
>      C  HC4
> ;;;;;;;
> 
> Is that reasonable?  Thanks for your help.
> 
> 

Seems fine to me.

-Justin

> On Mon, Oct 27, 2008 at 1:54 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     xianghong qi wrote:
> 
>         Hello,
> 
>         Could anyone give me some suggestions about how to write a
>         toplogy file for methane with OPLS-AA force field?
>         Thanks in advance.
> 
> 
>     For a very simple molecule like methane, it should be very
>     straightforward to do from reading Chapter 5.
> 
>     -Justin
> 
>         -Xianghong Qi
> 
>         -- 
>         Some people make the world more special just by being in it.
> 
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
> 
> -- 
> Some people make the world more special just by being in it.

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

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================