[gmx-users] gbsa.itp for amber ff

[Justin Lemkul]

On 2/25/13 10:05 PM, Yun Shi wrote:
> Hi all,
>
> If I want do MD simulation with amber ff and implicit solvent, would
> including gbsa.itp in .top file and specifying parameters in .mdp as
> follows be sufficient?
>
> implicit_solvent = GBSA
> gb_algorithm     = OBC
> nstgbradii	 = 1.0
> rgbradii         = 1.0

In my experience, only infinite cutoffs (rvdw=rcoulomb=rlist=rgbradii=0) lead to 
stable simulations.  In my hands, even commonly applied "long cutoffs" (2.0 - 
4.0 nm) lead to structural deformations.

> gb_epsilon_solvent = 78.3
> gb_dielectric_offset = 0.009
> sa_algorithm         = Ace-approximation
> sa_surface_tension   = 0.0054
>
>
> But I wonder if this line is problematic in gbsa.itp: ";Br
> 0.1      1      1        0.125     0.85 ; H". Is this for a bromine
> atom or hydrogen?
>

It's commented out, so it's irrelevant.  The line should probably be removed, 
though.

-Justin

> [ implicit_genborn_params ]
>
> ; atype      sar      st     pi       gbr	hct
> ;Br           0.1      1      1        0.125     0.85 ; H
> C            0.172    1      1.554    0.1875    0.72 ; C
> CA           0.18     1      1.037    0.1875    0.72 ; C
> ....
>
>
> Regards,
> Yun
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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