[gmx-users] (no subject)

[Justin Lemkul]

On 1/6/13 7:29 AM, fatemeh ramezani wrote:
>
>
> I didn't set epsilon and sigma between au and other atoms equal to zero, but I have not enteredanyEpsilon and Sigmafor them , and once again I set them zero and try it again.

If you didn't set them at all, grompp should have given a fatal error.

> But if closing of gold to protein, is because of charge, how do I delete its effect ? How can I uncharged the system? (Of course, the whole system charge that is shown in  the first grompp step is very low near -0.11).
>

If your system has a net charge of -0.11, the topology is incorrect.  Fractional 
charges on the system are nonphysical.

-Justin

-- 
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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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