[gmx-users] How to add iron parameter?

[Justin Lemkul]

On 10/15/14 2:05 PM, Johnny Lu wrote:
> Pure md doesn't deal with complex orbitals well, I guess. Hydrogen bonds in
> pure md is not directional, as it should be.
>
> can molecular dynamics (md) simulate heavy metals, like iron, which have d
> oribtals?
>
> I heard that even calcium is a bit troublesome in md.
>

Most multivalent ions are extremely poor representations in additive force 
fields.  I wouldn't trust any Fe3+ in an MM force field.

-Justin

> On Wed, Oct 15, 2014 at 1:22 PM, Guangyu Zhu <gzhu at hwi.buffalo.edu> wrote:
>
>> Hi, I’m a beginner of gromacs. I want to do simulation for a protein with
>> protein with ferrous or ferric. But there is no iron in force field. What
>> is easiest way to do it? Can I just add a few lines to aminocids.rtp, like
>> this?
>>
>> [FE]
>>
>>   [ atoms]
>>
>>     FE  FE    3.0000    0
>>
>>   [ bonds]
>>
>>   [ angles ]
>>
>>   [ impropers ]
>>
>>   [ dihedrals ]
>>
>>
>> Thanks!
>> Guangyu
>> --
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-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================