Re: AMBER: nucgen problem

From: <>
Date: Tue, 07 Jun 2005 19:48:13 +0000

1)I have pasted the input file which i gave to nucgen for 12mer.

  NUC 1
G5 C A A A A T T T T G C3

  NUC 2
C5 G T T T T A A A A C G3


2)Sir reg. my second question i have attached the pdb file here (GCAT). i
could understand that the numbering given by insightII is the problem
when it is read in xleap.can anyone help me in solving it.i used

Thank You,

On 6/7/2005, "David A. Case" <> wrote:

>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 - 20:53:00 PDT
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