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
--
========================================
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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