[gmx-users] topology file for methane.

[xianghong qi]

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.


On Mon, Oct 27, 2008 at 1:54 PM, Justin A. Lemkul <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 | (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.
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