[gmx-users] using gmxchek -f traj.trr -s1 topol.tpr

Grazia Daminelli Grazia.Daminelli-Widany at TU-Berlin.DE
Fri Feb 17 12:41:57 CET 2006


I am working on a protein (BMP-2) in water using the ffG43a1 force field 
and Gromacs 3.3.
After neutralizing the solvated protein (total charge of the protein is 
-8), I was running a 100-step energy minimization. Although the 
potential energy was going down, all bonded energy terms related to the 
protein were positive (order of 10^3). Trying to understand if something 
is wrong with my structure I was running the command *gmxcheck -f 
traj.trr -s1 topol.tpr * and I got a long list of the sort:

Distance between atoms 1 and 5 is 0.147, should be 0.022

If I look to my structure atom 1 and 5 are the N and CA atoms of a SER 
residue. A distance of 0.147 nm would be perfect, why should it be 0.022?

if I look to the ffG43a1.rtp file I see that the N CA bond in the SER 
residue is so defined:

[ SER ]


 [ bonds ]

    N     H    gb_2

    N    CA    gb_20


where gb_20  in ffG43a1bon.itp is:

#define gb_20       0.1470  8.7100e+06
; CHn  -  N, NT, NL, NZ, NE     900

where comes this 0.022 value from?



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