On 21/02/2012 8:39 AM, Talal Alotaibi wrote:
Hi,
I am trying to freeze the protein during equilibruim. I made the
energy minimization with no freezing. but when I freeze the protein
and try to do "grompp", it gives me this error:
A more sound protocol for preparation for MD probably involves the use
of position restraints, rather than frozen atoms. See various tutorials
for examples.
==============================================
Fatal error:
14623 atoms are not part of any of the T-Coupling groups
==============================================
What I did is I first made .ndx file that include the protein atoms.
Then, I wrote this in the comand:
grompp -f ----.mdp -c -----.gro -n ----.ndx -p ----.top -o ------.tpr
Copying and pasting actual command lines is preferred by those who might
give feedback. They want to see what actually happened, not what you
think happened.
-----.mdp: I include the freeze option in this file.
-----.ndx: This includes the group that I want to freeze.
1841: the total number of protein atoms.
116100: the total nuber of system atoms.
116100 < 14623. Some part of your report is badly wrong.
Mark
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