AMBER Archive (2005)

Subject: AMBER: Connecting two molecules

From: Hwankyu Lee (leehk_at_umich.edu)
Date: Mon May 23 2005 - 10:13:00 CDT

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.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu