[gmx-users] How to deal with phosphate radicals?

[Jinzhi Tan]

Dear gmx-users,

The 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. I wonder how to solve this problem and if
it is okay to delete all the hydrogen atoms in the phosphate radical.
Thank you very much for your answer and your kind help.

                            O-
                            |
    HPO3-  changes into     P―O
                             \ /
                              O

Best regards,
Jinzhi Tan
 

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Shanghai Institute of Meteria Medica
Chinese Academy of Sciences
Shanghai 201203, China
Tel：   +86-21-50806600-1201
E-mail: tanjinzhi at hotmail.com 
        jztan at mail.shcnc.ac.cn   
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