Thank You Azadeh, for your answer but actually in NAMD there is no .tpr file so the issue still remained the same.

But thank you for your answer.

Dear Samman,

First of all, the xst file must be read, in particular for the systems prepared in the CHARMM-GUI, using the following command:

pbc readxst *.xst

Later on, you can execute the following command to eliminate enlarged bond lengths:

pbc unwrap -all

If your problem is not related to the enlarged bond lengths, you can run the command given below.

pbc wrap -all -compound res -center bb -centersel "protein"