Re: Prevent DNA denaturation

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Thu Jun 06 2019 - 10:36:45 CDT

The `ssrestraints` plugin in VMD can help you automatically generate
extrabonds based restraints for DNA.

On Thu, Jun 6, 2019 at 11:32 AM Brian Radak <brian.radak_at_gmail.com> wrote:

> For atom groups, you can use colvars. For specific atom interactions I
> would recommend extraBonds. You can read about both in the user guide.
>
> HTH,
> BKR
>
> On Thu, Jun 6, 2019 at 9:19 AM Priyanka Mondal <pmondal_at_udel.edu> wrote:
>
>> Hi,
>> you can add harmonic restrain to specific atoms by changing their beta
>> value. The following tutorial uses that technique on silicon nitride
>> membrane.
>>
>> http://bionano.physics.illinois.edu/tutorials/modeling-nanopores-sequencing-dna
>>
>> Priyanka Mondal,
>> Department of Physics and Astronomy,
>> University of Delaware,
>> USA
>>
>>
>> On Thu, Jun 6, 2019 at 4:45 AM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp>
>> wrote:
>>
>>> Dear NAMD Users
>>>
>>> I have a question about how to add the (harmonic) interaction between
>>> several atoms which I specified.
>>>
>>> I want to restraint each base-pair of double-stranded DNA to prevent
>>> denaturation.
>>> Thus, I want to restrain the distance between a pair of atoms (C1' atoms
>>> in a DNA base-pair).
>>>
>>> Thank you in advance.
>>> Best wishes,
>>> Takeru Kameda
>>> PhD Student, Hiroshima University, Japan
>>>
>>>

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