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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