[gmx-users] Generating GROMACS input file from the GAMESS output file

Justin Lemkul jalemkul at vt.edu
Tue Jul 11 18:55:45 CEST 2017

On 7/10/17 2:32 AM, 조영래 wrote:
> Thank you Justin
> Every time your comment helped me.
> I should compare two system that are Zn_binding protein and Fe_binding
> protein.
> So I need force field that satisfies the following conditions.
> First, force field contains two metal ion (Fe and Zn)information.
> Second, force field contain metal ion binding mode amino acid information
> for example cysteine (CYM) in AMBER.
> However many force fields did not satisfied above conditions.
> So I would like to generate *.gro *itp file for metal atoms by GAMESS.
> But according to your comment this is not correct.
> In my case, the metal ions (Fe and Zn) binds one cysteine and two
> histidines.
> I want to simulate these complexes (i.e. Fe_protein and Zn_protein complex).
> Please suggest me an ideal force field that in able to be used for
> sumulation of the avode mentaioned complexes.

I don't know of one.  Dealing with transition metals is one of the hardest tasks 
in parametrization.  There's a reason why after many decades of development, the 
parameters still don't exist...  Depending on what you need to do, hybrid QM/MM 
is probably the best/most straightforward approach.  Classical force fields do 
not deal well with these kinds of systems.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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