AMBER: Connecting two molecules

From: Hwankyu Lee <leehk.umich.edu>
Date: Mon, 23 May 2005 11:13:00 -0400

Dear Amber-users,

When I tried to connect two molecules (connection between N and P,
shown in below), they were automatically disconnected when energy
minimization performed. This reaction happens in experiment, so there
is no doubt that this reaction is reasonable. I suspect that it might
happen because of bond formation of phosphate group. I guess that
phosphate group should have partial double bond, but I'm not sure that
my system has that. How can I approach to this problem? Is there any
function in xleap to make partial bonds? Does it happen automatically
in xleap? Do you have other opinions about this problem?

What I did in xleap were that....
1) I attached phosphate group into DNA.DG5.O5'. Before that, I
generated phosphate group in xleap, Phosphate group was treated as
non-DNA molecules, so I generated prepin and frcmod of phosphate group
by using antechamber.

2) Then, I needed to have more bond angle and dihedral parameters, so I
found those parameters by analogy with other parameters already in the
AMBER database, and upgraded .frcmod file.

3) Connect N and P, and then when I did energy minimization with
restraints of molecules, everything was fine. But, when I did
energy-minimization without restraints of molecules, the connection
between N and P was broken and went back to original configurations.

           H O
            | ||
---CH2-N P-O5'-DNA
                 |
                 OH

best,
Hwankyu.

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Received on Mon May 23 2005 - 16:53:00 PDT
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