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....
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