On Sun, Apr 08, 2012, mehdi bagherpoor wrote:
>
> I am using Amber software for DNA simulation. Specially in my project I
> need to fix two ends of DNA strands,The DNA that I want to simulate has 17
> sequence.
>
> I have used the two related manual of this package as explain below:
> 1. "*GROUP commands*":
> ------
> DNA 17-mer: 2ns MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 12.0, ntr = 0,
^^^^^^^^^^^
To use restraints (with either the group or the restraintmask syntax) you
need to set ntr=1, not 0.
Do a short run and examine the mdout file: it will tell you what restraints are
being used.
...good luck...dac
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Received on Sun Apr 08 2012 - 11:30:03 PDT
