From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Mar 04 2020 - 08:55:20 CST
If two atoms are supposed to have a bond, then you do not need extraBonds
or any other restraint. You need to tell the software that prepares the
topology (usually psfgen for NAMD) to create a bond between them. That is,
unless there are atoms missing from the PDB file that are supposed to be
between the two residues in question. Then you'll have to make up
coordinates from them (usually via a structural modeling software).
Be patient and try to spend more time on this problem, because for
atomistic simulations the correctness of the initial 3D structure and
connectivity is the most vital ingredient.
Giacomo
On Wed, Mar 4, 2020 at 9:44 AM soodabeh ghaffari <soodabehghaffari_at_gmail.com>
wrote:
> 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?
> *extraBonds*
> *extraBondsCosAngles*
> *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,
> Soodabeh
>
>
> On Wed, Mar 4, 2020 at 9:04 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> 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
>>
>
-- 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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