Carlos,
I am currently trying to calculate the pmf for the base flipping of a
thymine dimer out of the DNA duplex. I have been trying to do this with
a two dimensional coordinate, using torsions, but nothing seems to
produce the flipped-out state. From some previous work, I think that a
center of mass pseudodihedral will work, at least I hope so. I have a
16-mer of DNA, Na+ counterions and a water box (~4800 waters). Any help
is much appreciated.
Lauren O'Neil
Carlos Simmerling wrote:
> Lauren,
> we have some code that we've just developed for this and it's not
> yet user-friendly. It might work for you, but it depends a bit
> on how big your groups are, etc. Can you give me any info
> on what you need to do?
> carlos
>
> Lauren O'Neil wrote:
>
>> A quick question:
>>
>> Is it possible to setup a center of mass dihedral restraint in
>> amber? I know that this can be done for distances. I searched the
>> archive of the reflector and there was an unanswered message from
>> 2002 on this topic.
>> Thanks for the help...
>>
>> Lauren O'Neil
>> University of Notre Dame
>> Notre Dame, IN
>>
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>
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Received on Wed Sep 27 2006 - 06:07:13 PDT
