[gmx-users] problem with position-restrained dynamics of a charged system

[OZGE ENGIN]

Hi all,

I have a problem with position-restrained (pr) dynamics of a charged residue in a water box. Up to the position-restrained step, the method worked well; however, it gave the following error in the pr step:

Fatal error:
number of coordinates in coordinate file (lysine_b4pr.gro, 767)
             does not match topology (lysine.top, 0)

I could not understand the error because the lysine.top file has already contained the appropriate numbers of atoms defined for protein, ion, and solvent molecules. Moreover, I used the same topology file in the preceding step and it worked. So, what may be the problem?

Thanks in advance!

Ozge Engin