From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Mar 04 2020 - 08:03:49 CST
Hello Soodabeh, if these are not meant to be covalently bound (are they??),
the best option to create a new "peptide bond" sounds like extraBonds:
http://www.ks.uiuc.edu/Research/namd/2.13/ug/node27.html#SECTION00086400000000000000
Other more flexible but also more complex options are Colvars or tclForces:
http://www.ks.uiuc.edu/Research/namd/2.13/ug/node51.html
http://www.ks.uiuc.edu/Research/namd/2.13/ug/node48.html
On Wed, Mar 4, 2020 at 12:31 AM soodabeh ghaffari <
soodabehghaffari_at_gmail.com> wrote:
> Dear Sir/Madam,
> I have a pdb file in which two residues are not connected and their
> distances are greater than peptide bond. I want to do MD simulation and add
> constraint to MD.conf so that their distance should be with peptide bond
> and I have a connected pdb file at the end.
> Can you help me? which constraint should I have use and how?
> Do you have any example?
> Thanks
> Best Regards,
> Soodabeh
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Research collaborator, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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