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

[saurabh shakya]

hello,
the iron is bonded to the cystines sulfur ,the
hydrogens in question are the hydrogens attached to
the beta carbon,even reducing the time step to .2 fs
does not help . The em and md without this dihedral
runs fine but including the iron dihedrals gives rise
to lincs warning .The source of my starting structure
is a pdb file.

With best regards
Saurabh Kumar Shakya.

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