[gmx-users] about the phosphate radicals

[Jinzhi Tan]

Dear gmx-users,  

I encoutered a big problem when I deal with my small molecule. My ligand contains two phosphate radicals. One is inside of protein,
and the other is exposed to water. There is no problem with the first phosphate radical. While the latter changes into three-membered circle as soon as energy minimization is performed if there is one H atom within the phosphate radical (As the following form). I wonder how to solve this problem and if it is okay to delete all the hydrogen atoms in the phosphate radical.
 

                            O-
                            |
    HPO3-  changes into     P―O
                             \ /
                              O
Thank you very much for your answer and your kind help.  

Best regards,
Jinzhi Tan
2004-5-11