Re: adding peptide constraint in NAMD configuration file

From: soodabeh ghaffari (
Date: Wed Mar 04 2020 - 08:44:22 CST

Hello Dr Fiorin,
These two atoms ( backbone N of one residue and carbonyl carbon of the
other) should be covalently bound but in my pdb file they are not. Is
extraBonds fine(the first link you provided)?Do you have any example of
usage of extraBonds?

1. If so, how I can get the parameters k, ref, n. And how can I select atom?

2.Is this right to add these line to MD.conf?
*extraBondsFile myfile.txt*

3. In myfile.txt,is <atom> atom serial number in pdb file? and <ref> is the
bond length?
bond <atom> <atom> <k> <ref>
For instance, is it right to write below(if atom serial number is 100 and
and 101 and k=250 and bond length should be 1.3 (but currently, it is more
than 1.3))?
bond 100 101 250 1.3

4.and one more question, the location of myfile.txt should be the same as
conf file?

I appreciate your help
Thank you so much
Best Regards,

On Wed, Mar 4, 2020 at 9:04 AM Giacomo Fiorin <>

> 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:
> Other more flexible but also more complex options are Colvars or tclForces:
> On Wed, Mar 4, 2020 at 12:31 AM soodabeh ghaffari <
>> 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

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