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

[Mark Abraham]

sangeeta kundu wrote:

a) Temperature coupling groups must include all atoms in the system. Do 
not couple handfuls of atoms separately. So "Protein" and "Non-Protein" 
are often right.

b) If you use -n you need to supply an index file, which you might make 
with make_ndx. That index file must define all groups referred to above. 
These groups need not correspond to molecules, residues or anything 
else, so anything pdb2gmx said is not strictly relevant.

Mark

> 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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> 
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