[gmx-users] query about simulation of a protein containg a metal ion

[sangeeta kundu]

Dear Sir,
    

    I want to simulate a protein with a CA2+ ion and one crystal water using G431 force field, simulation of the protein without the metal ion went off successfully,But while running the simulation with the metal ion it's giving  a fatal error during position restrained molecular dynamics, 

"Fatal error:
Group CA2+ not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.
In that case use the '-n' option.
"
Upto energy minimisation I have modified aminoacids.dat and other required files, & it's not giving  any error messege. During PR dynamics it's giving an error messege 
"-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: readir.c, line: 1075

Fatal error:
1 atoms are not part of any of the T-Coupling groups
-------------------------------------------------------
"
 If I incorporate CA2+ ion in the mdp file it's giving "Fatal error:
Group CA2+ not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.
In that case use the '-n' option.
"
if I use -n option it's giving
-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: futil.c, line: 330

File input/output error:
index.ndx
-------------------------------------------------------
I don't understand what else files should be considered and manually edited..Please help.While running pdb2gmx CA2+ ion is considered as follows.

type    resnr residue
CA2+      CA    CA

Please suggest what should be taken into account while running the simulation with the metal ion.


regards
Sangeeta Kundu



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