Dear Dr. Chuang,
You can try restraining the terminal base pairs either with the belly
option (ibelly=1) or harmonic restraints (ntr=1). I had the same problem a
while ago and this worked for me; I have not yet found any other solution
but will let you know if I do.
Good luck!
Sincerely,
Michael G. Cooney
Postdoctoral Associate
Dept. of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602, USA
On Sat, 17 Mar 2001, Xiaolin Chuang wrote:
> Dear AMBERs,
>
> I have a big problem (for me). I have run MD of DNA(10pair). After running
> production (100 ps), I found that one strand of DNA was out of the box (in
> input file I set iwrap=0). My questions are;
>
> 1. I used 'ptraj' with trajectory file to bring the molecule back togetter
> (in amber manual, this is use for visualization, no effect of energy). But I
> found that the RMSd of original trajectory differed from RMSd of the new
> trajectory obtaining from 'ptraj program'. Moreover, I tried to calculate
> energy of each snapshot and I obtained the difference results from original
> and new trajectories. WHY?
>
> 2. How to setup input file to aviod separating of two strands? or do you
> have any suggestion?
>
> -----------
> 3. In input file if I set 'iwrap=1', I know that the coordinates will be
> wrapped into the box. But I don't know what is the disadvantage of running
> MD, e.g. time or energy, for setting iwrap=1?
>
> 4. If I set nstlim=2 and iwrap=1, what does sander use coordinates for
> running step 2, wrapped coord. or unwrapped coord.?
>
> -----------
>
> Thank you very much for reading my long questions and for your respondence.
>
> Thank you,
> Xiaolin
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Received on Wed Mar 21 2001 - 09:43:18 PST
