[gmx-users] polymer charmm27 parameter

[Mijiddorj B]

Dear Justin,

Thank you very much for your reply.
I prepared 3 residues including a middle and two end units for charmm22. I
also used the swissparam for their atom type and the partial charges. Now,
Gmx is working fine with the residues. Is it right? Thank you again.

Best regards,
Mijiddorj

------------------------------
>
> Message: 5
> Date: Mon, 11 Nov 2019 20:16:27 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] polymer charmm27 parameter
> Message-ID: <76526271-8832-1f53-877a-6fceb6206044 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/11/19 10:05 AM, Mijiddorj B wrote:
> > Dear Prof. Justin,
> >
> > Thank you very much for your reply. My target polymer is the branched
> > polyethyleneimine. I copied a figure. I am sorry for furthermore asking.
> If
> > I understand correctly, the model compound consists of the last two heavy
> > atoms and first two heavy atoms along with the corresponding protons. Is
> it
> > right?
>
> Whatever model compounds you use have to encompass all relevant internal
> degrees of freedom (bonds, angles, dihedrals).
>
> > Do I need to make a model N and C terminal atoms?
>
> You need termini, but N- and C-termini are protein-specific concepts, so
> no, not exactly. See e.g.
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html
>
> -Justin
>
> > Thank you for your time.
> >
> > [image: image.png]
> >
> > Best regards,
> >
> > Mijiddorj
> >
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Sun, 10 Nov 2019 09:20:52 -0500
> >> From: Justin Lemkul <jalemkul at vt.edu>
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] polymer charmm27 parameter
> >> Message-ID: <4ed3e913-bf3d-f79d-e997-fc03d451edcd at vt.edu>
> >> Content-Type: text/plain; charset=utf-8; format=flowed
> >>
> >>
> >>
> >> On 11/10/19 8:52 AM, Mijiddorj B wrote:
> >>> Dear GMX users,
> >>>
> >>> I would like to simulate a long polymer, which consists of the number
> of
> >>> units (monomers). I generated the charmm27 parameter for the single
> unit
> >>> using swissparam server.
> >>> However, I need to prepare the parameter for the long polymer chain.
> >>> If you have any experience, please advise me to build the topology of
> the
> >>> long polymer using the parameter of the single unit. Thanks for any
> >>> guidance.
> >> You need a model compound that captures all relevant degrees of freedom,
> >> including bonds, angles, and dihedrals between monomer units. You then
> >> need to parametrize those interactions so the properties of your chain
> >> are correct.
> >>
> >> -Justin
> >>
> >>
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 187, Issue 28
> ******************************************************
>