AMBER Archive (2005)

Subject: Re: AMBER: nucgen problem

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Tue Jun 07 2005 - 14:34:17 CDT

doesn't the residue name format have to be (A4,1x)?
I am not sure if that makes a difference but your file looks like (A4)
carlos

cbala_at_igib.res.in wrote:

>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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