[gmx-users] tip3p.itp => OWT3, HW vs. ffG53a6nb.itp => OW, H
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 5 13:14:08 CET 2008
Chih-Ying Lin wrote:
> 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.
> Thank you
> [ 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
> 1 OWT3 1 SOL OW 1 -0.834
> 2 HW 1 SOL HW1 1 0.417
> 3 HW 1 SOL HW2 1 0.417
> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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