Zhong Zheng wrote:
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?
Once written to the energy file, no, the energy terms cannot be separated.
2. How can I fix this error? Do I have to put all the backbone atoms in
the same charge group?
You are going to have a problem any time you try to split charge groups between
energy groups. MainChain does not include H atoms, thus you are seeing the
error you describe above.
Ask yourself if it is meaningful to analyze energies of an incomplete group
(i.e., those that have had bonds to neighboring atoms broken). To do what you
are thinking of, you will at least have to use the MainChain+H group, but that
may fail as well, depending on how the charge groups are set up.
-Justin
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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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