[gmx-users] How to add iron parameter?

[Johnny Lu]

not sure if this helps. But maillist once mentioned parameter for heme
(that are not necessary good):

http://comments.gmane.org/gmane.science.biology.gromacs.user/59978
http://ccl.net/chemistry/resources/messages/2008/09/22.001-dir/index.html
https://www.mail-archive.com/gmx-users@gromacs.org/msg24046.html

On Wed, Oct 15, 2014 at 2:05 PM, Johnny Lu <johnny.lu128 at gmail.com> 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.
>
> 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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>
>