AMBER Archive (2006)

Subject: Re: AMBER: center of mass dihedral restraints

From: venditti2_at_unisi.it
Date: Mon Sep 25 2006 - 12:44:01 CDT

A new dihedral angle has been recently used to carry out base flipping
studies in AMBER.

Barthel and Zacharias (2006), Biophys. J., 90, 2450-2462.

I hope this can help.
-Vincenzo

> 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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