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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