[gmx-users] tip3p.itp => OWT3, HW vs. ffG53a6nb.itp => OW, H

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> Hi
> Here are part of tip3p.itp and ffG53a6nb.itp.
> tip3p.itp => OWT3, HW
> ffG53a6nb.itp => OW, H
> 
> To make the simulation run, I attempt to replace OWT3 and HW with OW
> and H in my tip3p.itp file. Does it make sense ?
> 

No.  What you are doing is cannabilizing the parameters.  In ffG53a6, OW and H 
correspond to SPC water oxygen and hydrogen.  So you would be applying TIP3P 
charges with SPC LJ parameters.  This makes no sense.

> 
> In tip3p.itp, OWT3, HW are not defined in a specific / limited force field ??
> 

 From tip3p.itp, you should be able to see that the parameters correspond to 
OPLS-AA, although I believe it could also be made to work with AMBER as well.

-Justin

> 
> Thank you
> Lin
> 
> 
> 
> 
> 
> 
> 
> 
> [ atoms ]
> ; id    at type res nr  residu name     at name         cg nr   charge
> #ifdef _FF_OPLS
> 1     opls_111  1       SOL              OW             1       -0.834
> 2     opls_112  1       SOL             HW1             1        0.417
> 3     opls_112  1       SOL             HW2             1        0.417
> #else
> 1       OWT3    1       SOL              OW             1       -0.834
> 2       HW      1       SOL             HW1             1        0.417
> 3       HW      1       SOL             HW2             1        0.417
> #endif
> 
> 
> 
> 
> 
>    OW    8      0.000      0.000     A  0.0026173456  2.634129e-06
>     HC    1      0.000      0.000     A   8.464e-05  1.5129e-08
>     H    1      0.000      0.000     A           0           0
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-- 
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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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