[gmx-users] Ryckeart Bellemans parameters for Fe coupled to cystines

[Anton Feenstra]

saurabh shakya wrote:
> Hello,
> I am trying to perform a MD simulation on a protein
> with Fe coupled to cystines . I have made all the
> necessary additions to the topology file like
> bonds,pairs,angles but I am not sure how to add the
> Ryckeart Bellemans parameters for the dihedral for
> this additional Fe .  Specifying the dihedral as a
> proper dihedral (type 1) always leads to links error
> with the hydrogens of cystines rotating more than 30
> degrees. Can I specify dihedral as proper(type 1) in
> place of RB type (type 3).
> Any suggestion is welcome.

I'm not sure that I understand the problem. Some more questions:
1) why do you have hydrogens on the cystines? I'd think you would have
    the iron connected to the sulphur, without any hydrogens.
2) why do you use R-B dihedrals? Is that because otherwise you get
    Lincs warnings? In that case, probably the error is somewhere else
    in your topology (or starting structure). Can you run (MD or EM)
    without this dihedral at all?
3) Have you (carefully) checked your starting structure for strange
    things (e.g., bad contacts)? What is the source of your starting
    structure?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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