[gmx-users] About ADP

[Zhiguo Liu]

Dear gmx-users ，
    I want to produce topol file of ADP with dundee server, what kind of protonate state should be choosed? that is, how many protons should be added to the negative "O" in "P-O-"?

           _
          O
          |  _
        O=P-O
          |    
          O
          |  _
        O=P-O
          |
          O
          |
         ...
         (1)

           
          OH
          |  _
        O=P-O
          |
          O
          |  _
        O=P-O
          |
          O
          |
         ...
         (2)


that equals to say, (1) or (2) should be choosed for the dundee server input?


Best Regard!
                                 Zhiguo Liu
                                 DDDC
                                 Chinese Academy of Science
                                 Shanghai,China
                                 zgliu at iris3.simm.ac.cn
                                 2004-03-14