Zhong Zheng wrote:
hi all
I have an isolated iron in the protein. If I don't' put that iron in,
everything runs through fine. However, if I put the iron in, the mdrun
step (doing energy minimization) will clash. It says segmentation fault
and lots of LINCS WARNING. The iron has a +2 charge with four His
ligands and one Glu ligand. The total charge for the complex should be
+1. Is there a good way to treat this isolated iron?
You may be in for some parameterization, which, for transition metals, can be
quite complicated:
http://wiki.gromacs.org/index.php/Parameterization
http://wiki.gromacs.org/index.php/Exotic_Species
-Justin
Thanks a lot.
Zhong Zheng
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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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