Dear all
I have successfully run though the energy minimization on my target
protein. I am trying to extract the backbone-backbone interactions
from the energy output files. My understanding is that I need to
define the energy groups in the grompp.mdp. This is what I edited:
energygrps = mainchain
I also have the index file ready. "mainchain" is defined in it which
is actually a default group. However I am getting the following error
message when I move on to run grompp (grompp -n *.ndx) :
atoms 1 and 2 in charge group 1 of molecule type 'Protein_L' are in
different energy groups
Atom 1&2 are the N and H1 in an Ala. They are defined in one charge
group. If I manually modify the topol file and make them into
different charge groups, the program will move on and complain about
another two atoms. However, the backbone atoms (N C CA O) ARE put in
different charge group in the opls force field I am using.
So my questions are:
1. Can I extract the backbone-backbone interactions directly using
g_energy or some other commands?
2. How can I fix this error? Do I have to put all the backbone atoms
in the same charge group?
Many thanks.
Zhong Zheng
Ph.D candidate
Physics Dept., City College-CUNY
Marshak Science Building J-419 ,
160 Convent Ave,
New York, NY 10031 USA
Tel: (212)650-6079
MCCE new wiki: http://134.74.90.158/
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