[gmx-users] cofactor in PDB file (again)

[Alok]

Hi  Gromaxians,
               I haven't received any replies regarding my previous post on the same subject.
I will try to be more elaborate on the problem if i was not very clear the first time round.

I have some doubts regarding simulation of my system with cofactors
and also about some suggestions on references of simulations on such systems.

First Question
##############

I have two Ca ions as a cofactor with my protein in the PDB file.

while using PDB2GMX, Should i define protein & cofactor (i.e. Ca) together in the same
chain in the input PDB file or should i have to define different chain ID for Protein & 
Ca ions so as to distinguish them .

To be more clear on my problem, i define my PDB and topology file as below:

First: when i define protein and cofactor (Ca ions) in the same chain id of the input PDB file.

Eg: a section of my input PDB file

ATOM   1728 1HB  CYS   118      25.225 110.035  -3.752  1.00 13.23      
ATOM   1729 2HB  CYS   118      24.087 108.787  -4.276  1.00 13.23   
TER    1729      CYS   118                                            
HETATM 1730 CA   CA2+  201      22.164  99.781   1.304  0.92 15.78      
HETATM 1882 CA   CA2+  401      31.452 105.664   2.892  0.76 20.43      
HETATM 1731  O   HOH   202      20.707  99.706   3.256  0.89 16.45   
HETATM 1732  O   HOH   203      23.256  97.570   1.747  0.91 16.77      

Eg: a section of the topology file.
[ molecules ]
; Compound        #mols
Protein             1      (total 118 Protein Residues +2 Ca =120 residues)
SOL               151      (crystal water molecules present in PDB file)

Second: WHen i define protein and cofactor (Ca ions) in different chain id of the input PDB file.

Eg: a section of my input PDB file

ATOM   1726  H   CYS  A 118      26.489 111.329  -5.466  1.00  9.69      
ATOM   1727  HA  CYS  A 118      25.013 108.997  -6.671  1.00 11.08      
ATOM   1728 1HB  CYS  A 118      25.225 110.035  -3.752  1.00 13.23      
ATOM   1729 2HB  CYS  A 118      24.087 108.787  -4.276  1.00 13.23      
TER    1729      CYS  A 118                                              
HETATM 1730 CA   CA2+ B 201      22.164  99.781   1.304  0.92 15.78     
HETATM 1882 CA   CA2+ B 401      31.452 105.664   2.892  0.76 20.43     
HETATM 1731  O   HOH    202      20.707  99.706   3.256  0.89 16.45     
HETATM 1732  O   HOH    203      23.256  97.570   1.747  0.91 16.77      

Eg: A section of the topology file.

[ molecules ]
; Compound        #mols
Protein_A           1      (total 156 residues)
Protein_B           1      (2 Ca ions)
SOL               151      (crystal water molecules present in PDB file)

So which of these two options should i follow in defining my system???

Second Question
###############

Also I would like to know if there are any reported  simulation of a system in which Ca/Mg/Zn ions are present 
as cofactors.

I would be extremely thankfull if anyone could could suggest me any reference(s) of papers published on simulations
of system with these ions as cofactors.

Actually I am little apprehensive about the force field parameters of these ions as i have not come accross papers
on simulation with these ions present..

please guide me to overcome these situations.

Thanks in Advance.

Alok Jain