AMBER Archive (2005)

Subject: Re: AMBER: nucgen problem

From: cbala_at_igib.res.in
Date: Tue Jun 07 2005 - 14:48:13 CDT


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

  NUC 1
D
G5 C A A A A T T T T G C3

  NUC 2
D
C5 G T T T T A A A A C G3

END
$ABDNA

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
leaprc.ff99.

Thank You,
c.bala

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

>On Tue, Jun 07, 2005, cbala_at_igib.res.in 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?
>
>....dac
>
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  • application/msword attachment: GCAT.doc

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