[gmx-users] minimization

[Morteza Khabiri]

Dear MARK and Tsjerk

I found something....after making topology file by pdb2gmx ... I made tpr
file by grompp ... then I give the original pdb file and tpr file to ngmx
to see the system before running minimization...the interesting thing was
that the bonds between atoms are stretched......
I compare the atoms of amino acids in topology file with the topolgy file
of other proteins which did not have any problem...the oplss number for
all atoms is the same....
but still I could not understand where is the problem....

thanks