Dear Shipra,  I supposed (but not sure) that when you talk about clashes of COOH group you mean the O-C-O or H-O-C angles or the C-CO-OH out-of-plane improper dihedral are strongly distorted, is it correct ? Distortions from equilibrium values may be "physiological" as a consequence of the thermal motion and are normally detected in the structure of single MD snapshots. On the other hand, they could be also "pathological" and indicative of some problems in the parametrization of that structure frame.

I suggest to first check (may be you just did it) the ff parameters assigned to that COOH group. If parametrization might be correct, I suggest to calculate the time averaged structure of that COOH group, you may find that the averaged structure has no distortion (and that your simulation is ok).

Not familiar with Gromacs, but I did find unusual conformation in AMBER. And I found the reason for that was the force field parameters on that group were wrong. You'd better check the atom type of atoms in COOH group to see if there's anything wrong.

I am also not familiar Gromacs but when you said -COOH I guess you protonated GLU with using some patch. If that is the case, did you regenerate all angles dihedrals after applying the patch while building the structure? If you haven't; some unusual conformations will appear while minimizing and subsequent MD.

Dear Atanu,

I protonated the GLU but not the unusual conformation residue (protonated residue is near by GLU53, Glu45). GLU53, Glu45 residues have unusual conformation. Is there any need to regenerate all angles while building model, if protonated residue is not same?

Thanks.