[gmx-users] Questions about energy groups!

Zhong Zheng zhozheng at gmail.com
Sun Mar 22 15:56:09 CET 2009

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
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