[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer

Mijiddorj B b.mijiddorj at gmail.com
Thu Nov 21 02:51:57 CET 2019


Dear Prof. Justin,

Thank you very much for your reply. I would like to use charmm27 because my
system contains a surface model, which were parametrized by INTERFACE Force
Field and compatible with charmm27. The polymer parameters of charmm27 were
generated by swissparam, and the server renamed the atomtypes. I would like
to assign those parameters with original charmm27. If possible, I would
like to use original charmm27 parameters instead of the values of
swissparam. I used charmm36 atomtypes for clarification.
I do not know the atom type of the nitrogen which connected with three
carbons.

Best regards,

Mijiddorj

------------------------------
>
> Message: 5
> Date: Wed, 20 Nov 2019 20:19:16 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments
>         for polymer
> Message-ID: <7db2548d-f487-a34b-f27f-0f876aa202ca at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/19/19 9:54 PM, Mijiddorj B wrote:
> > Dear Gmx users,
> >
> > Currently, I am trying to assign the atomtypes in charmm27 for the
> > polyethyleneimine polymer. It includes several different groups of
> atoms. I
> > included following illustration and asignment:
> > ##############################################
> >                           H                     CH2
> >                           |                     /
> > NH2--CH2--CH2--N--CH2--CH2--N--CH2 ...
> >
> > ##############################################
> > I assigned and the charmm27 atomtypes as following and compared charmm36
> > atomtypes generated by CgenFF.
> > Atom       Charmm27     Charmm36
> > N (NH2) ---> NH2       |    NG321
> > N (NH1) ---> NH1       |    NG311
> > C (CH2) ---> CT2       |    CG321
> > H (HC2) ---> HA         |    HGA2
> > N                 ?           |    NG301
> >
> > If you have any experience, please check my assignments the charmm27 atom
> > types and advice me the atomtype of the last Nitrogen, which were
> assigned
> > as NG301 with CgenFF.
>
> Why are you replacing the CGenFF atom types? The replacements you are
> making completely change the LJ terms and therefore render the dihedral
> parameters invalid. There is no need to make these changes, just use the
> CGenFF atom types in your simulation (all of which is contained in the
> CHARMM36 port, which you should use rather than the outdated CHARMM27
> force field files).
>
> -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
>
> ==================================================
>
>
>
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