[gmx-users] cofactor in PDB file

Alok alokjain at iitk.ac.in
Thu Jun 9 09:41:35 CEST 2005

Hi  Gromaxians,

I have some doubts regarding cofactors presents in PDB file .
I have two Ca ions as a cofactor with my protein . Now i want to know
should i consider protein & cofactor (i.e. Ca) together or should i have to
define different chain ID for Protein & Ca to distinguish them .

I mean which (bottom of top file) one is more suitable from both of them
pasted at below.

[ molecules ]
; Compound        #mols
Protein             1      (total 156 Protein Residues +2 Ca =158 residues)
SOL               151      (crystal water molecules present in PDB 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)

My second question regarding any reference for these type of simulation
i.e. is any any-one reported any simulation in which Ca or Mg or Zn ions
present in its original PDB file. Actually i want to know is any one
published any Article which validates the force field parameters for these

please guide me to overcome these situations.

Thanks in Advance.

Alok Jain

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