VMD-L Mailing List

From: Edelmiro Moman (edelmiro.moman_at_gmail.com)
Date: Sat Aug 21 2010 - 04:03:35 CDT

If you are going to use explicit solvation, keep in mind that cations
are important to stabilise the DNA structure. Namely, K+, Mg++ and
Mn++. Have a look to the relevant literature. It may be a good idea to
pay attention to the initial placement of the counterions around the
DNA (there are some programs to do that, either empirically-based or
electrostatic potential-based). Pre-equilibrating solvent+ions while
keeping your biomolecule rigid is also an option to be considered.
Obviously, the choice of force field is important, check what it has
been recently done concerning nucleic acids simulations.

On Sat, Aug 21, 2010 at 9:14 AM, Ajasja Ljubetič
<ajasja.ljubetic_at_gmail.com> wrote:
> Fix or restraint the DNA
> backbone. http://www.ks.uiuc.edu/Research/namd/2.7b3/ug/node26.html
> Or better yet solvate the system first and minimize afterwards.
> regards,
> Ajasja
> On Sat, Aug 21, 2010 at 05:39, Janani.S <011213028_at_bioinfo.sastra.edu>
> wrote:
>>
>> How to do prevent distortion of a molecule while doing energy
>> minimisation?
>> I am trying to minimise a protein-dna sequence invaccuo ( dielectric 1).
>> But the dna gets very badly distorted. How can i prevent this?
>> - Janani
> 

-- 
Edelmiro Moman, PhD
Campus Limpertsberg, BRB 1.11B
Luxembourg Centre for Systems Biomedicine (LCSB)
162a avenue de la Faïencerie
L-1511 Luxembourg
Phone : +352 46-66-44-6117
E-mail : Eldemiro.Moman at uni.lu
http://wwwen.uni.lu/lcsb
http://www.edelmiromoman.eu/