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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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
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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
========================================
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