Re: AMBER: nucgen problem

From: David A. Case <>
Date: Tue, 7 Jun 2005 07:38:15 -0700

On Tue, Jun 07, 2005, wrote:
> 1) i constructed a 12mer DNA duplex using 'nucgen' program. the program
> runs fine and it has successfully created the pdb file but when i view
> the pdb file, overlapping of bases is seen at some base pairs, 4 out of
> 12 base pairs, it occurs in both GC and AT pairs, can anyone suggest
> what could be the reason for this and how i can avoid it.

Can you post your nucgen input?

> 2) i constructed a B-DNA duplex (10 mer) in insightII and i loaded in
> xleap after deleting all hydrogens, but xleap adds one phosphite at the
> 5' positions of both the strands, can anyone help in solving this
> problem.

Which leaprc file did you load? What is the residue name in the pdb file
at the 5' position?


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Received on Tue Jun 07 2005 - 15:53:00 PDT
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